Analysing the Requirements for an Open Research Knowledge Graph: Use Cases, Quality Requirements and Construction Strategies

Current science communication has a number of drawbacks and bottlenecks which have been subject of discussion lately: Among others, the rising number of published articles makes it nearly impossible to get a full overview of the state of the art in a certain field, or reproducibility is hampered by fixed-length, document-based publications which normally cannot cover all details of a research work. Recently, several initiatives have proposed knowledge graphs (KG) for organising scientific information as a solution to many of the current issues. The focus of these proposals is, however, usually restricted to very specific use cases. In this paper, we aim to transcend this limited perspective and present a comprehensive analysis of requirements for an Open Research Knowledge Graph (ORKG) by (a) collecting and reviewing daily core tasks of a scientist, (b) establishing their consequential requirements for a KG-based system, (c) identifying overlaps and specificities, and their coverage in current solutions. As a result, we map necessary and desirable requirements for successful KG-based science communication, derive implications, and outline possible solutions.

Graphing Contributions in Natural Language Processing Research: Intra-Annotator Agreement on a Trial Dataset

Purpose: To stabilize the NLPContributionGraph scheme for the surface structuring of contributions information in Natural Language Processing (NLP) scholarly articles via a two-stage annotation methodology: first stage - to define the scheme; and second stage - to stabilize the graphing model. Approach: Re-annotate, a second time, the contributions-pertinent information across 50 prior-annotated NLP scholarly articles in terms of a data pipeline comprising: contribution-centered sentences, phrases, and triples. To this end specifically, care was taken in the second annotation stage to reduce annotation noise while formulating the guidelines for our proposed novel NLP contributions structuring scheme. Findings: The application of NLPContributionGraph on the 50 articles resulted in finally in a dataset of 900 contribution-focused sentences, 4,702 contribution-information-centered phrases, and 2,980 surface-structured triples. The intra-annotation agreement between the first and second stages, in terms of F1, was 67.92% for sentences, 41.82% for phrases, and 22.31% for triples indicating that with an increased granularity of the information, the annotation decision variance is greater. Practical Implications: Demonstrate NLPContributionGraph data integrated in the Open Research Knowledge Graph (ORKG), a next-generation KG-based digital library with compute enabled over structured scholarly knowledge, as a viable aid to assist researchers in their day-to-day tasks. Value: NLPContributionGraph is a novel scheme to obtain research contribution-centered graphs from NLP articles which to the best of our knowledge does not exist in the community. And our quantitative evaluations over the two-stage annotation tasks offer insights into task difficulty.

SciBERT-based Semantification of Bioassays in the Open Research Knowledge Graph

As a novel contribution to the problem of semantifying biological assays, in this paper, we propose a neural-network-based approach to automatically semantify, thereby structure, unstructured bioassay text descriptions. Experimental evaluations, to this end, show promise as the neural-based semantification significantly outperforms a naive frequency-based baseline approach. Specifically, the neural method attains 72% F1 versus 47% F1 from the frequency-based method.

NLPContributions: An Annotation Scheme for Machine Reading of Scholarly Contributions in Natural Language Processing Literature

We describe an annotation initiative to capture the scholarly contributions in natural language processing (NLP) articles, particularly, for the articles that discuss machine learning (ML) approaches for various information extraction tasks. We develop the annotation task based on a pilot annotation exercise on 50 NLP-ML scholarly articles presenting contributions to the five information extraction tasks 1. machine translation, 2. named entity recognition, 3. question answering, 4. relation classification, and 5. text classification. In this article, we describe the outcomes of this pilot annotation phase. Through the exercise we have obtained an annotation methodology; and found eight core information units that reflect the contribution of the NLP-ML scholarly investigations. The resulting annotation scheme we developed based on these information units is called NLPContributions. The overarching goal of our endeavor is: 1) to find a systematic set of patterns of subject-predicate-object statements for the semantic structuring of scholarly contributions that are more or less generically applicable for NLP-ML research articles; 2) to apply the discovered patterns in the creation of a larger annotated dataset for training machine readers of research contributions; 3) to ingest the dataset into the Open Research Knowledge Graph (ORKG) infrastructure as a showcase for creating user-friendly state-of-the-art overviews; 4) to integrate the machine readers into the ORKG to assist users in the manual curation of their respective article contributions. We envision that the NLPContributions methodology engenders a wider discussion on the topic toward its further refinement and development. Our pilot annotated dataset of 50 NLP-ML scholarly articles per the NLPContributions scheme is available at https://github.com/jenlindadsouza/NLPContributions.

Question Answering on Scholarly Knowledge Graphs

Answering questions on scholarly knowledge comprising text and other artifacts is a vital part of any research life cycle. Querying scholarly knowledge and retrieving suitable answers is currently hardly possible due to the following primary reason: machine inactionable, ambiguous and unstructured content in publications. We present JarvisQA, a BERT based system to answer questions on tabular views of scholarly knowledge graphs. Such tables can be found in a variety of shapes in the scholarly literature (e.g., surveys, comparisons or results). Our system can retrieve direct answers to a variety of different questions asked on tabular data in articles. Furthermore, we present a preliminary dataset of related tables and a corresponding set of natural language questions. This dataset is used as a benchmark for our system and can be reused by others. Additionally, JarvisQA is evaluated on two datasets against other baselines and shows an improvement of two to three folds in performance compared to related methods.

Improving Scholarly Knowledge Representation: Evaluating BERT-based Models for Scientific Relation Classification

With the rapidly growing number of research publications, there is a vast amount of scholarly information that needs to be organized in digital libraries. To deal with this challenge, digital libraries use semantic techniques to build knowledge-base structures for organizing scientific information. Identifying relations between scientific terms can help with the construction of a representative knowledge-based structure. While advanced automated techniques have been developed for relation extraction, many of these techniques were evaluated under different scenarios, which limits their comparability. To this end, this study presents a thorough empirical evaluation of eight Bert-based classification models by exploring two factors: 1) Bert model variants, and 2) classification strategies. To simulate real-world settings, we conduct our sentence-level assessment using the abstracts of scholarly publications in three corpora, two of which are distinct corpora and the third of which is the union of the first two. Our findings show that SciBert models perform better than Bert-BASE models. The strategy of classifying a single relation each time is preferred in the corpus consisting of abundant scientific relations, while the strategy of identifying multiple relations at one time is beneficial to the corpus with sparse relations. Our results offer recommendations to the stakeholders of digital libraries for selecting the appropriate technique to build a structured knowledge-based system for the ease of scholarly information organization.

The STEM-ECR Dataset: Grounding Scientific Entity References in STEM Scholarly Content to Authoritative Encyclopedic and Lexicographic Sources

We introduce the STEM (Science, Technology, Engineering, and Medicine) Dataset for Scientific Entity Extraction, Classification, and Resolution, version 1.0 (STEM-ECR v1.0). The STEM-ECR v1.0 dataset has been developed to provide a benchmark for the evaluation of scientific entity extraction, classification, and resolution tasks in a domain-independent fashion. It comprises abstracts in 10 STEM disciplines that were found to be the most prolific ones on a major publishing platform. We describe the creation of such a multidisciplinary corpus and highlight the obtained findings in terms of the following features: 1) a generic conceptual formalism for scientific entities in a multidisciplinary scientific context; 2) the feasibility of the domain-independent human annotation of scientific entities under such a generic formalism; 3) a performance benchmark obtainable for automatic extraction of multidisciplinary scientific entities using BERT-based neural models; 4) a delineated 3-step entity resolution procedure for human annotation of the scientific entities via encyclopedic entity linking and lexicographic word sense disambiguation; and 5) human evaluations of Babelfy returned encyclopedic links and lexicographic senses for our entities. Our findings cumulatively indicate that human annotation and automatic learning of multidisciplinary scientific concepts as well as their semantic disambiguation in a wide-ranging setting as STEM is reasonable.

The Query Translation Landscape: a Survey

Whereas the availability of data has seen a manyfold increase in past years, its value can be only shown if the data variety is effectively tackled ---one of the prominent Big Data challenges. The lack of data interoperability limits the potential of its collective use for novel applications. Achieving interoperability through the full transformation and integration of diverse data structures remains an ideal that is hard, if not impossible, to achieve. Instead, methods that can simultaneously interpret different types of data available in different data structures and formats have been explored. On the other hand, many query languages have been designed to enable users to interact with the data, from relational, to object-oriented, to hierarchical, to the multitude emerging NoSQL languages. Therefore, the interoperability issue could be solved not by enforcing physical data transformation, but by looking at techniques that are able to query heterogeneous sources using one uniform language. Both industry and research communities have been keen to develop such techniques, which require the translation of a chosen 'universal' query language to the various data model specific query languages that make the underlying data accessible. In this article, we survey more than forty query translation methods and tools for popular query languages, and classify them according to eight criteria. In particular, we study which query language is a most suitable candidate for that 'universal' query language. Further, the results enable us to discover the weakly addressed and unexplored translation paths, to discover gaps and to learn lessons that can benefit future research in the area.

Towards a Knowledge Graph based Speech Interface

Applications which use human speech as an input require a speech interface with high recognition accuracy. The words or phrases in the recognised text are annotated with a machine-understandable meaning and linked to knowledge graphs for further processing by the target application. These semantic annotations of recognised words can be represented as a subject-predicate-object triples which collectively form a graph often referred to as a knowledge graph. This type of knowledge representation facilitates to use speech interfaces with any spoken input application, since the information is represented in logical, semantic form, retrieving and storing can be followed using any web standard query languages. In this work, we develop a methodology for linking speech input to knowledge graphs and study the impact of recognition errors in the overall process. We show that for a corpus with lower WER, the annotation and linking of entities to the DBpedia knowledge graph is considerable. DBpedia Spotlight, a tool to interlink text documents with the linked open data is used to link the speech recognition output to the DBpedia knowledge graph. Such a knowledge-based speech recognition interface is useful for applications such as question answering or spoken dialog systems.