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Markus Stocker

Publications and source records attributed to Markus Stocker.

At least 19 recordsLinked to original sources

Nested Named Entity Recognition in Plasma Physics Research Articles

Named Entity Recognition (NER) is an important task in natural language processing that aims to identify and extract key entities from unstructured text. We present a novel application of NER in plasma physics research articles and address the challenges of extracting specialized entities from scientific text in this domain. Research articles in plasma physics often contain highly complex and context-rich content that must be extracted to enable, e.g., advanced search. We propose a lightweight approach based on encoder-transformers and conditional random fields to extract (nested) named entities from plasma physics research articles. First, we annotate a plasma physics corpus with 16 classes specifically designed for the nested NER task. Second, we evaluate an entity-specific model specialization approach, where independent BERT-CRF models are trained to recognize individual entity types in plasma physics text. Third, we integrate an optimization process to systematically fine-tune hyperparameters and enhance model performance. Our work contributes to the advancement of entity recognition in plasma physics and also provides a foundation to support researchers in navigating and analyzing scientific literature.

cs.CL

dtreg: Describing Data Analysis in Machine-Readable Format in Python and R

For scientific knowledge to be findable, accessible, interoperable, and reusable, it needs to be machine-readable. Moving forward from post-publication extraction of knowledge, we adopted a pre-publication approach to write research findings in a machine-readable format at early stages of data analysis. For this purpose, we developed the package dtreg in Python and R. Registered and persistently identified data types, aka schemata, which dtreg applies to describe data analysis in a machine-readable format, cover the most widely used statistical tests and machine learning methods. The package supports (i) downloading a relevant schema as a mutable instance of a Python or R class, (ii) populating the instance object with metadata about data analysis, and (iii) converting the object into a lightweight Linked Data format. This paper outlines the background of our approach, explains the code architecture, and illustrates the functionality of dtreg with a machine-readable description of a t-test on Iris Data. We suggest that the dtreg package can enhance the methodological repertoire of researchers aiming to adhere to the FAIR principles.

cs.DL

Enhancing Information Retrieval in Digital Libraries through Unit Harmonisation in Scholarly Knowledge Graphs

Scientists have always used the studies and research of other researchers to achieve new objectives and perspectives. In particular, employing and operating the measured data in previous studies is so practical. Searching the content of other scientists' articles is a challenge that researchers have always struggled with. Nowadays, the use of knowledge graphs as a semantic database has helped a lot in saving and retrieving scholarly knowledge. Such technologies are crucial to upgrading traditional search systems to smart knowledge retrieval, which is crucial to getting the most relevant answers for a user query, especially in information and knowledge management. However, in most cases, only the metadata of a paper is searchable, and it is still cumbersome for scientists to have access to the content of the papers. In this paper, we present a novel method of faceted search \emph{structured content} for comparing and filtering measured data in scholarly knowledge graphs while different units of measurement are used in different studies. This search system proposes applicable units as facets to the user and would dynamically integrate content from further remote knowledge graphs to materialize the scholarly knowledge graph and achieve a higher order of exploration usability on scholarly content, which can be filtered to better satisfy the user's information needs. The state of the art is that, by using our faceted search system, users can not only search the contents of scientific articles, but also compare and filter heterogeneous data.

cs.DL

Advancing Scientific Knowledge Retrieval and Reuse with a Novel Digital Library for Machine-Readable Knowledge

Digital libraries for research, such as the ACM Digital Library or Semantic Scholar, do not enable the machine-supported, efficient reuse of scientific knowledge (e.g., in synthesis research). This is because these libraries are based on document-centric models with narrative text knowledge expressions that require manual or semi-automated knowledge extraction, structuring, and organization. We present ORKG reborn, an emerging digital library that supports finding, accessing, and reusing accurate, fine-grained, and reproducible machine-readable expressions of scientific knowledge that relate scientific statements and their supporting evidence in terms of data and code. The rich expressions of scientific knowledge are published as reborn (born-reusable) articles and provide novel possibilities for scientific knowledge retrieval, for instance by statistical methods, software packages, variables, or data matching specific constraints. We describe the proposed system and demonstrate its practical viability and potential for information retrieval in contrast to state-of-the-art digital libraries and document-centric scholarly communication using several published articles in research fields ranging from computer science to soil science. Our work underscores the enormous potential of scientific knowledge databases and a viable approach to their construction.

cs.IR

Managing Comprehensive Research Instrument Descriptions within a Scholarly Knowledge Graph

In research, measuring instruments play a crucial role in producing the data that underpin scientific discoveries. Information about instruments is essential in data interpretation and, thus, knowledge production. However, if at all available and accessible, such information is scattered across numerous data sources. Relating the relevant details, e.g. instrument specifications or calibrations, with associated research assets (data, but also operating infrastructures) is challenging. Moreover, understanding the (possible) use of instruments is essential for researchers in experiment design and execution. To address these challenges, we propose a Knowledge Graph (KG) based approach for representing, publishing, and using information, extracted from various data sources, about instruments and associated scholarly artefacts. The resulting KG serves as a foundation for exploring and gaining a deeper understanding of the use and role of instruments in research, discovering relations between instruments and associated artefacts (articles and datasets), and opens the possibility to quantify the impact of instruments in research.

cs.DL

Research Knowledge Graphs: the Shifting Paradigm of Scholarly Information Representation

Sharing and reusing research artifacts, such as datasets, publications, or methods is a fundamental part of scientific activity, where heterogeneity of resources and metadata and the common practice of capturing information in unstructured publications pose crucial challenges. Reproducibility of research and finding state-of-the-art methods or data have become increasingly challenging. In this context, the concept of Research Knowledge Graphs (RKGs) has emerged, aiming at providing an easy to use and machine-actionable representation of research artifacts and their relations. That is facilitated through the use of established principles for data representation, the consistent adoption of globally unique persistent identifiers and the reuse and linking of vocabularies and data. This paper provides the first conceptualisation of the RKG vision, a categorisation of in-use RKGs together with a description of RKG building blocks and principles. We also survey real-world RKG implementations differing with respect to scale, schema, data, used vocabulary, and reliability of the contained data. We also characterise different RKG construction methodologies and provide a forward-looking perspective on the diverse applications, opportunities, and challenges associated with the RKG vision.

cs.IR

SciCom Wiki: Fact-Checking and FAIR Knowledge Distribution for Scientific Videos and Podcasts

Democratic societies need accessible, reliable information. Videos and Podcasts have established themselves as the medium of choice for civic dissemination, but also as carriers of misinformation. The emerging Science Communication Knowledge Infrastructure (SciCom KI) curating non-textual media is still fragmented and not adequately equipped to scale against the content flood. Our work sets out to support the SciCom KI with a central, collaborative platform, the SciCom Wiki, to facilitate FAIR (findable, accessible, interoperable, reusable) media representation and the fact-checking of their content, particularly for videos and podcasts. Building an open-source service system centered around Wikibase, we survey requirements from 53 stakeholders, refine these in 11 interviews, and evaluate our prototype based on these requirements with another 14 participants. To address the most requested feature, fact-checking, we developed a neurosymbolic computational fact-checking approach, converting heterogenous media into knowledge graphs. This increases machine-readability and allows comparing statements against equally represented ground-truth. Our computational fact-checking tool was iteratively evaluated through 10 expert interviews, a public user survey with 43 participants verified the necessity and usability of our tool. Overall, our findings identified several needs to systematically support the SciCom KI. The SciCom Wiki, as a FAIR digital library complementing our neurosymbolic computational fact-checking framework, was found suitable to address the raised requirements. Further, we identified that the SciCom KI is severely underdeveloped regarding FAIR knowledge and related systems facilitating its collaborative creation and curation. Our system can provide a central knowledge node, yet a collaborative effort is required to scale against the imminent (mis-)information flood.

cs.DL

Computational Fact-Checking of Online Discourse: Scoring scientific accuracy in climate change related news articles

Democratic societies need reliable information. Misinformation in popular media, such as news articles or videos, threatens to impair civic discourse. Citizens are, unfortunately, not equipped to verify the flood of content consumed daily at increasing rates. This work aims to quantify the scientific accuracy of online media semi-automatically. We investigate the state of the art of climate-related ground truth knowledge representation. By semantifying media content of unknown veracity, their statements can be compared against these ground truth knowledge graphs. We implemented a workflow using LLM-based statement extraction and knowledge graph analysis. Our implementation can streamline content processing towards state-of-the-art knowledge representation and veracity quantification. Developed and evaluated with the help of 27 experts and detailed interviews with 10, the tool evidently provides a beneficial veracity indication. These findings are supported by 43 anonymous participants from a parallel user survey. This initial step, however, is unable to annotate public media at the required granularity and scale. Additionally, the identified state of climate change knowledge graphs is vastly insufficient to support this neurosymbolic fact-checking approach. Further work towards a FAIR (Findable, Accessible, Interoperable, Reusable) ground truth and complementary metrics is required to support civic discourse scientifically.

cs.CL

Rethinking the production and publication of machine-reusable expressions of research findings

Literature is the primary expression of scientific knowledge and an important source of research data. However, scientific knowledge expressed in narrative text documents is not inherently machine reusable. To facilitate knowledge reuse, e.g. for synthesis research, scientific knowledge must be extracted from articles and organized into databases post-publication. The high time costs and inaccuracies associated with completing these activities manually has driven the development of techniques that automate knowledge extraction. Tackling the problem with a different mindset, we propose a pre-publication approach, known as reborn, that ensures scientific knowledge is born reusable, i.e. produced in a machine-reusable format during knowledge production. We implement the approach using the Open Research Knowledge Graph infrastructure for FAIR scientific knowledge organization. We test the approach with three use cases, and discuss the role of publishers and editors in scaling the approach. Our results suggest that the proposed approach is superior compared to classical manual and semi-automated post-publication extraction techniques in terms of knowledge richness and accuracy as well as technological simplicity.

cs.DL

Scholarly Knowledge Graph Construction from Published Software Packages

The value of structured scholarly knowledge for research and society at large is well understood, but producing scholarly knowledge (i.e., knowledge traditionally published in articles) in structured form remains a challenge. We propose an approach for automatically extracting scholarly knowledge from published software packages by static analysis of their metadata and contents (scripts and data) and populating a scholarly knowledge graph with the extracted knowledge. Our approach is based on mining scientific software packages linked to article publications by extracting metadata and analyzing the Abstract Syntax Tree (AST) of the source code to obtain information about the used and produced data as well as operations performed on data. The resulting knowledge graph includes articles, software packages metadata, and computational techniques applied to input data utilized as materials in research work. The knowledge graph also includes the results reported as scholarly knowledge in articles.

cs.DL

Scholarly Knowledge Extraction from Published Software Packages

A plethora of scientific software packages are published in repositories, e.g., Zenodo and figshare. These software packages are crucial for the reproducibility of published research. As an additional route to scholarly knowledge graph construction, we propose an approach for automated extraction of machine actionable (structured) scholarly knowledge from published software packages by static analysis of their (meta)data and contents (in particular scripts in languages such as Python). The approach can be summarized as follows. First, we extract metadata information (software description, programming languages, related references) from software packages by leveraging the Software Metadata Extraction Framework (SOMEF) and the GitHub API. Second, we analyze the extracted metadata to find the research articles associated with the corresponding software repository. Third, for software contained in published packages, we create and analyze the Abstract Syntax Tree (AST) representation to extract information about the procedures performed on data. Fourth, we search the extracted information in the full text of related articles to constrain the extracted information to scholarly knowledge, i.e. information published in the scholarly literature. Finally, we publish the extracted machine actionable scholarly knowledge in the Open Research Knowledge Graph (ORKG).

cs.DL

MORTY: Structured Summarization for Targeted Information Extraction from Scholarly Articles

Information extraction from scholarly articles is a challenging task due to the sizable document length and implicit information hidden in text, figures, and citations. Scholarly information extraction has various applications in exploration, archival, and curation services for digital libraries and knowledge management systems. We present MORTY, an information extraction technique that creates structured summaries of text from scholarly articles. Our approach condenses the article's full-text to property-value pairs as a segmented text snippet called structured summary. We also present a sizable scholarly dataset combining structured summaries retrieved from a scholarly knowledge graph and corresponding publicly available scientific articles, which we openly publish as a resource for the research community. Our results show that structured summarization is a suitable approach for targeted information extraction that complements other commonly used methods such as question answering and named entity recognition.

cs.CL

Persistent Identification and Interlinking of FAIR Scholarly Knowledge

We leverage the Open Research Knowledge Graph - a scholarly infrastructure that supports the creation, curation, and reuse of structured, semantic scholarly knowledge - and present an approach for persistent identification of FAIR scholarly knowledge. We propose a DOI-based persistent identification of ORKG Papers, which are machine-actionable descriptions of the essential information published in scholarly articles. This enables the citability of FAIR scholarly knowledge and its discovery in global scholarly communication infrastructures (e.g., DataCite, OpenAIRE, and ORCID). While publishing, the state of the ORKG Paper is saved and cannot be further edited. To allow for updating published versions, ORKG supports creating new versions, which are linked in provenance chains. We demonstrate the linking of FAIR scholarly knowledge with digital artefacts (articles), agents (researchers) and other objects (organizations). We persistently identify FAIR scholarly knowledge (namely, ORKG Papers and ORKG Comparisons as collections of ORKG Papers) by leveraging DataCite services. Given the existing interoperability between DataCite, Crossref, OpenAIRE and ORCID, sharing metadata with DataCite ensures global findability of FAIR scholarly knowledge in scholarly communication infrastructures.

cs.DL

Open Research Knowledge Graph:A System Walkthrough

Despite improved digital access to scholarly literature in the last decades, the fundamental principles of scholarly communication remain unchanged and continue to be largely document-based. Scholarly knowledge remains locked in representations that are inadequate for machine processing. The Open Research Knowledge Graph (ORKG) is an infrastructure for representing, curating and exploring scholarly knowledge in a machine actionable manner. We demonstrate the core functionality of ORKG for representing research contributions published in scholarly articles. A video of the demonstration and the system are available online.

cs.DL

Plumber: A Modular Framework to Create Information Extraction Pipelines

Information Extraction (IE) tasks are commonly studied topics in various domains of research. Hence, the community continuously produces multiple techniques, solutions, and tools to perform such tasks. However, running those tools and integrating them within existing infrastructure requires time, expertise, and resources. One pertinent task here is triples extraction and linking, where structured triples are extracted from a text and aligned to an existing Knowledge Graph (KG). In this paper, we present PLUMBER, the first framework that allows users to manually and automatically create suitable IE pipelines from a community-created pool of tools to perform triple extraction and alignment on unstructured text. Our approach provides an interactive medium to alter the pipelines and perform IE tasks. A short video to show the working of the framework for different use-cases is available online under: https://www.youtube.com/watch?v=XC9rJNIUv8g

cs.CL

TinyGenius: Intertwining Natural Language Processing with Microtask Crowdsourcing for Scholarly Knowledge Graph Creation

As the number of published scholarly articles grows steadily each year, new methods are needed to organize scholarly knowledge so that it can be more efficiently discovered and used. Natural Language Processing (NLP) techniques are able to autonomously process scholarly articles at scale and to create machine readable representations of the article content. However, autonomous NLP methods are by far not sufficiently accurate to create a high-quality knowledge graph. Yet quality is crucial for the graph to be useful in practice. We present TinyGenius, a methodology to validate NLP-extracted scholarly knowledge statements using microtasks performed with crowdsourcing. The scholarly context in which the crowd workers operate has multiple challenges. The explainability of the employed NLP methods is crucial to provide context in order to support the decision process of crowd workers. We employed TinyGenius to populate a paper-centric knowledge graph, using five distinct NLP methods. In the end, the resulting knowledge graph serves as a digital library for scholarly articles.

cs.DL

The Digitalization of Bioassays in the Open Research Knowledge Graph

Background: Recent years are seeing a growing impetus in the semantification of scholarly knowledge at the fine-grained level of scientific entities in knowledge graphs. The Open Research Knowledge Graph (ORKG) https://www.orkg.org/ represents an important step in this direction, with thousands of scholarly contributions as structured, fine-grained, machine-readable data. There is a need, however, to engender change in traditional community practices of recording contributions as unstructured, non-machine-readable text. For this in turn, there is a strong need for AI tools designed for scientists that permit easy and accurate semantification of their scholarly contributions. We present one such tool, ORKG-assays. Implementation: ORKG-assays is a freely available AI micro-service in ORKG written in Python designed to assist scientists obtain semantified bioassays as a set of triples. It uses an AI-based clustering algorithm which on gold-standard evaluations over 900 bioassays with 5,514 unique property-value pairs for 103 predicates shows competitive performance. Results and Discussion: As a result, semantified assay collections can be surveyed on the ORKG platform via tabulation or chart-based visualizations of key property values of the chemicals and compounds offering smart knowledge access to biochemists and pharmaceutical researchers in the advancement of drug development.

cs.DL

Enriching Scholarly Knowledge with Context

Leveraging a GraphQL-based federated query service that integrates multiple scholarly communication infrastructures (specifically, DataCite, ORCID, ROR, OpenAIRE, Semantic Scholar, Wikidata and Altmetric), we develop a novel web widget based approach for the presentation of scholarly knowledge with rich contextual information. We implement the proposed approach in the Open Research Knowledge Graph (ORKG) and showcase it on three kinds of widgets. First, we devise a widget for the ORKG paper view that presents contextual information about related datasets, software, project information, topics, and metrics. Second, we extend the ORKG contributor profile view with contextual information including authored articles, developed software, linked projects, and research interests. Third, we advance ORKG comparison faceted search by introducing contextual facets (e.g. citations). As a result, the devised approach enables presenting ORKG scholarly knowledge flexibly enriched with contextual information sourced in a federated manner from numerous technologically heterogeneous scholarly communication infrastructures.

cs.DL