Advanced omics technologies and facilities generate a wealth of valuable data daily; however, the data often lacks the essential metadata required for researchers to find and search them effectively. The lack of metadata poses a significant challenge in the utilization of these datasets. Machine learning-based metadata extraction techniques have emerged as a potentially viable approach to automatically annotating scientific datasets with the metadata necessary for enabling effective search. Text labeling, usually performed manually, plays a crucial role in validating machine-extracted metadata. However, manual labeling is time-consuming; thus, there is an need to develop automated text labeling techniques in order to accelerate the process of scientific innovation. This need is particularly urgent in fields such as environmental genomics and microbiome science, which have historically received less attention in terms of metadata curation and creation of gold-standard text mining datasets.
In this paper, we present two novel automated text labeling approaches for the validation of ML-generated metadata for unlabeled texts, with specific applications in environmental genomics. Our techniques show the potential of two new ways to leverage existing information about the unlabeled texts and the scientific domain. The first technique exploits relationships between different types of data sources related to the same research study, such as publications and proposals. The second technique takes advantage of domain-specific controlled vocabularies or ontologies. In this paper, we detail applying these approaches for ML-generated metadata validation. Our results show that the proposed label assignment approaches can generate both generic and highly-specific text labels for the unlabeled texts, with up to 44% of the labels matching with those suggested by a ML keyword extraction algorithm.
In this paper, we present a keyphrase generation approach using conditional Generative Adversarial Networks (GAN). In our GAN model, the generator outputs a sequence of keyphrases based on the title and abstract of a scientific article. The discriminator learns to distinguish between machine-generated and human-curated keyphrases. We evaluate this approach on standard benchmark datasets. Our model achieves state-of-the-art performance in generation of abstractive keyphrases and is also comparable to the best performing extractive techniques. We also demonstrate that our method generates more d…
Indian Institute of Technology, Gandhinagar（甘地纳加尔印度理工学院）
Automatic scientific keyphrase extraction is a challenging problem facilitating several downstream scholarly tasks like search, recommendation, and ranking. In this paper, we introduce SEAL, a scholarly tool for automatic keyphrase extraction and classification. The keyphrase extraction module comprises two-stage neural architecture composed of Bidirectional Long Short-Term Memory cells augmented with Conditional Random Fields. The classification module comprises of a Random Forest classifier. We extensively experiment to showcase the robustness of the system. We evaluate multiple state-of-the…
LS2N, Université de Nantes（南特大学LS2N实验室）；National Institute of Informatics（国立信息学研究所）
Sequence-to-sequence models have lead to significant progress in keyphrase generation, but it remains unknown whether they are reliable enough to be beneficial for document retrieval. This study provides empirical evidence that such models can significantly improve retrieval performance, and introduces a new extrinsic evaluation framework that allows for a better understanding of the limitations of keyphrase generation models. Using this framework, we point out and discuss the difficulties encountered with supplementing documents with -- not present in text -- keyphrases, and generalizing mode…
Keyphrase generation is the task of predicting a set of lexical units that conveys the main content of a source text. Existing datasets for keyphrase generation are only readily available for the scholarly domain and include non-expert annotations. In this paper we present KPTimes, a large-scale dataset of news texts paired with editor-curated keyphrases. Exploring the dataset, we show how editors tag documents, and how their annotations differ from those found in existing datasets. We also train and evaluate state-of-the-art neural keyphrase generation models on KPTimes to gain insights on ho…
Institute of Formal and Applied Linguistics, Charles University（查尔斯大学形式与应用语言学研究所）
Authors' keyphrases assigned to scientific articles are essential for recognizing content and topic aspects. Most of the proposed supervised and unsupervised methods for keyphrase generation are unable to produce terms that are valuable but do not appear in the text. In this paper, we explore the possibility of considering the keyphrase string as an abstractive summary of the title and the abstract. First, we collect, process and release a large dataset of scientific paper metadata that contains 2.2 million records. Then we experiment with popular text summarization neural architectures. Despi…
Kansas State University（堪萨斯州立大学）；University of Illinois at Chicago（伊利诺伊大学芝加哥分校）
While keyphrase extraction has received considerable attention in recent years, relatively few studies exist on extracting keyphrases from social media platforms such as Twitter, and even fewer for extracting disaster-related keyphrases from such sources. During a disaster, keyphrases can be extremely useful for filtering relevant tweets that can enhance situational awareness. Previously, joint training of two different layers of a stacked Recurrent Neural Network for keyword discovery and keyphrase extraction had been shown to be effective in extracting keyphrases from general Twitter data. W…
This paper studies keyphrase extraction in real-world scenarios where documents are from diverse domains and have variant content quality. We curate and release OpenKP, a large scale open domain keyphrase extraction dataset with near one hundred thousand web documents and expert keyphrase annotations. To handle the variations of domain and content quality, we develop BLING-KPE, a neural keyphrase extraction model that goes beyond language understanding using visual presentations of documents and weak supervision from search queries. Experimental results on OpenKP confirm the effectiveness of B…
Scientific digital libraries play a critical role in the development and dissemination of scientific literature. Despite dedicated search engines, retrieving relevant publications from the ever-growing body of scientific literature remains challenging and time-consuming. Indexing scientific articles is indeed a difficult matter, and current models solely rely on a small portion of the articles (title and abstract) and on author-assigned keyphrases when available. This results in a frustratingly limited access to scientific knowledge. The goal of the DELICES project is to address this pitfall b…
Jožef Stefan Institute（约瑟夫·斯蒂芬研究所）；Jožef Stefan International Postgraduate School（约瑟夫·斯蒂芬国际研究生院）；University of Maribor（马里博尔大学）
The COVID-19 pandemic triggered a wave of novel scientific literature that is impossible to inspect and study in a reasonable time frame manually. Current machine learning methods offer to project such body of literature into the vector space, where similar documents are located close to each other, offering an insightful exploration of scientific papers and other knowledge sources associated with COVID-19. However, to start searching, such texts need to be appropriately annotated, which is seldom the case due to the lack of human resources. In our system, the current body of COVID-19-related …
Nanjing University of Science and Technology（南京理工大学）
The premise of manual keyphrase annotation is to read the corresponding content of an annotated object. Intuitively, when we read, more important words will occupy a longer reading time. Hence, by leveraging human reading time, we can find the salient words in the corresponding content. However, previous studies on keyphrase extraction ignore human reading features. In this article, we aim to leverage human reading time to extract keyphrases from microblog posts. There are two main tasks in this study. One is to determine how to measure the time spent by a human on reading a word. We use eye f…
Automated methods for granular categorization of large corpora of text documents have become increasingly more important with the rate scientific, news, medical, and web documents are growing in the last few years. Automatic keyphrase extraction (AKE) aims to automatically detect a small set of single or multi-words from within a single textual document that captures the main topics of the document. AKE plays an important role in various NLP and information retrieval tasks such as document summarization and categorization, full-text indexing, and article recommendation. Due to the lack of suff…
Finding relevant scientific articles is crucial for advancing knowledge. Recommendation systems are helpful for such purpose, although they have only been applied to science recently. This article describes EILEEN (Exploratory Innovator of LitEraturE Networks), a recommendation system for scientific publications and grants with open source code and datasets. We describe EILEEN's architecture for ingesting and processing documents and modeling the recommendation system and keyphrase estimator. Using a unique dataset of log-in user behavior, we validate our recommendation system against Latent S…
TIB Leibniz Information Centre for Science and Technology（莱布尼茨科学与技术信息中心（TIB））
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 f…
FlyAOC: Evaluating Agentic Ontology Curation of Drosophila Scientific Knowledge Bases
University of Michigan（密歇根大学）；University of Illinois Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）；University of California, Berkeley（加州大学伯克利分校）；University of Washington（华盛顿大学）
TIB – Leibniz Information Centre for Science and Technology（莱布尼茨科技信息中心）；L3S Research Center（L3S研究中心）
Sequential sentence classification deals with the categorisation of sentences based on their content and context. Applied to scientific texts, it enables the automatic structuring of research papers and the improvement of academic search engines. However, previous work has not investigated the potential of transfer learning for sentence classification across different scientific domains and the issue of different text structure of full papers and abstracts. In this paper, we derive seven related research questions and present several contributions to address them: First, we suggest a novel uni…
We examine the novel task of domain-independent scientific concept extraction from abstracts of scholarly articles and present two contributions. First, we suggest a set of generic scientific concepts that have been identified in a systematic annotation process. This set of concepts is utilised to annotate a corpus of scientific abstracts from 10 domains of Science, Technology and Medicine at the phrasal level in a joint effort with domain experts. The resulting dataset is used in a set of benchmark experiments to (a) provide baseline performance for this task, (b) examine the transferability …
University of Rostock（罗斯托克大学）；GESIS - Leibniz Institute for the Social Sciences（莱布尼茨社会科学研究所）；Heinrich-Heine-University（海因里希·海涅大学）
Knowledge about software used in scientific investigations is important for several reasons, for instance, to enable an understanding of provenance and methods involved in data handling. However, software is usually not formally cited, but rather mentioned informally within the scholarly description of the investigation, raising the need for automatic information extraction and disambiguation. Given the lack of reliable ground truth data, we present SoMeSci (Software Mentions in Science) a gold standard knowledge graph of software mentions in scientific articles. It contains high quality annot…
