Sören Auer


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Large Language Models for Scientific Information Extraction: An Empirical Study for Virology
Mahsa Shamsabadi | Jennifer D’Souza | Sören Auer
Findings of the Association for Computational Linguistics: EACL 2024

In this paper, we champion the use of structured and semantic content representation of discourse-based scholarly communication, inspired by tools like Wikipedia infoboxes or structured Amazon product descriptions. These representations provide users with a concise overview, aiding scientists in navigating the dense academic landscape. Our novel automated approach leverages the robust text generation capabilities of LLMs to produce structured scholarly contribution summaries, offering both a practical solution and insights into LLMs’ emergent abilities.For LLMs, the prime focus is on improving their general intelligence as conversational agents. We argue that these models can also be applied effectively in information extraction (IE), specifically in complex IE tasks within terse domains like Science. This paradigm shift replaces the traditional modular, pipelined machine learning approach with a simpler objective expressed through instructions. Our results show that finetuned FLAN-T5 with 1000x fewer parameters than the state-of-the-art GPT-davinci is competitive for the task.


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SemEval-2021 Task 11: NLPContributionGraph - Structuring Scholarly NLP Contributions for a Research Knowledge Graph
Jennifer D’Souza | Sören Auer | Ted Pedersen
Proceedings of the 15th International Workshop on Semantic Evaluation (SemEval-2021)

There is currently a gap between the natural language expression of scholarly publications and their structured semantic content modeling to enable intelligent content search. With the volume of research growing exponentially every year, a search feature operating over semantically structured content is compelling. The SemEval-2021 Shared Task NLPContributionGraph (a.k.a. ‘the NCG task’) tasks participants to develop automated systems that structure contributions from NLP scholarly articles in the English language. Being the first-of-its-kind in the SemEval series, the task released structured data from NLP scholarly articles at three levels of information granularity, i.e. at sentence-level, phrase-level, and phrases organized as triples toward Knowledge Graph (KG) building. The sentence-level annotations comprised the few sentences about the article’s contribution. The phrase-level annotations were scientific term and predicate phrases from the contribution sentences. Finally, the triples constituted the research overview KG. For the Shared Task, participating systems were then expected to automatically classify contribution sentences, extract scientific terms and relations from the sentences, and organize them as KG triples. Overall, the task drew a strong participation demographic of seven teams and 27 participants. The best end-to-end task system classified contribution sentences at 57.27% F1, phrases at 46.41% F1, and triples at 22.28% F1. While the absolute performance to generate triples remains low, as conclusion to the article, the difficulty of producing such data and as a consequence of modeling it is highlighted.


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The STEM-ECR Dataset: Grounding Scientific Entity References in STEM Scholarly Content to Authoritative Encyclopedic and Lexicographic Sources
Jennifer D’Souza | Anett Hoppe | Arthur Brack | Mohmad Yaser Jaradeh | Sören Auer | Ralph Ewerth
Proceedings of the Twelfth Language Resources and Evaluation Conference

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.

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Fine-tuning BERT with Focus Words for Explanation Regeneration
Isaiah Onando Mulang’ | Jennifer D’Souza | Sören Auer
Proceedings of the Ninth Joint Conference on Lexical and Computational Semantics

Explanation generation introduced as the world tree corpus (Jansen et al., 2018) is an emerging NLP task involving multi-hop inference for explaining the correct answer in multiple-choice QA. It is a challenging task evidenced by low state-of-the-art performances(below 60% in F-score) demonstrated on the task. Of the state-of-the-art approaches, fine-tuned transformer-based (Vaswani et al., 2017) BERT models have shown great promise toward continued system performance improvements compared with approaches relying on surface-level cues alone that demonstrate performance saturation. In this work, we take a novel direction by addressing a particular linguistic characteristic of the data — we introduce a novel and lightweight focus feature in the transformer-based model and examine task improvements. Our evaluations reveal a significantly positive impact of this lightweight focus feature achieving the highest scores, second only to a significantly computationally intensive system.


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Old is Gold: Linguistic Driven Approach for Entity and Relation Linking of Short Text
Ahmad Sakor | Isaiah Onando Mulang’ | Kuldeep Singh | Saeedeh Shekarpour | Maria Esther Vidal | Jens Lehmann | Sören Auer
Proceedings of the 2019 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Volume 1 (Long and Short Papers)

Short texts challenge NLP tasks such as named entity recognition, disambiguation, linking and relation inference because they do not provide sufficient context or are partially malformed (e.g. wrt. capitalization, long tail entities, implicit relations). In this work, we present the Falcon approach which effectively maps entities and relations within a short text to its mentions of a background knowledge graph. Falcon overcomes the challenges of short text using a light-weight linguistic approach relying on a background knowledge graph. Falcon performs joint entity and relation linking of a short text by leveraging several fundamental principles of English morphology (e.g. compounding, headword identification) and utilizes an extended knowledge graph created by merging entities and relations from various knowledge sources. It uses the context of entities for finding relations and does not require training data. Our empirical study using several standard benchmarks and datasets show that Falcon significantly outperforms state-of-the-art entity and relation linking for short text query inventories.

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Team SVMrank: Leveraging Feature-rich Support Vector Machines for Ranking Explanations to Elementary Science Questions
Jennifer D’Souza | Isaiah Onando Mulang’ | Sören Auer
Proceedings of the Thirteenth Workshop on Graph-Based Methods for Natural Language Processing (TextGraphs-13)

The TextGraphs 2019 Shared Task on Multi-Hop Inference for Explanation Regeneration (MIER-19) tackles explanation generation for answers to elementary science questions. It builds on the AI2 Reasoning Challenge 2018 (ARC-18) which was organized as an advanced question answering task on a dataset of elementary science questions. The ARC-18 questions were shown to be hard to answer with systems focusing on surface-level cues alone, instead requiring far more powerful knowledge and reasoning. To address MIER-19, we adopt a hybrid pipelined architecture comprising a featurerich learning-to-rank (LTR) machine learning model, followed by a rule-based system for reranking the LTR model predictions. Our system was ranked fourth in the official evaluation, scoring close to the second and third ranked teams, achieving 39.4% MAP.