Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userAn Information Extraction and Knowledge Graph Platform for Accelerating Biochemical Discoveries
148
0
0.0
(
0
)
Added by
Matteo Manica
Publication date
2019
fields
Informatics Engineering
and research's language is
English
Ask ChatGPT about the research
No Arabic abstract
Information extraction and data mining in biochemical literature is a daunting task that demands resource-intensive computation and appropriate means to scale knowledge ingestion. Being able to leverage this immense source of technical information helps to drastically reduce costs and time to solution in multiple application fields from food safety to pharmaceutics. We present a scalable document ingestion system that integrates data from databases and publications (in PDF format) in a biochemistry knowledge graph (BCKG). The BCKG is a comprehensive source of knowledge that can be queried to retrieve known biochemical facts and to generate novel insights. After describing the knowledge ingestion framework, we showcase an application of our system in the field of carbohydrate enzymes. The BCKG represents a way to scale knowledge ingestion and automatically exploit prior knowledge to accelerate discovery in biochemical sciences.
rate research
Read More
The coronavirus disease (COVID-19) has claimed the lives of over 350,000 people and infected more than 6 million people worldwide. Several search engines have surfaced to provide researchers with additional tools to find and retrieve information from the rapidly growing corpora on COVID-19. These engines lack extraction and visualization tools necessary to retrieve and interpret complex relations inherent to scientific literature. Moreover, because these engines mainly rely upon semantic information, their ability to capture complex global relationships across documents is limited, which reduces the quality of similarity-based article recommendations for users. In this work, we present the COVID-19 Knowledge Graph (CKG), a heterogeneous graph for extracting and visualizing complex relationships between COVID-19 scientific articles. The CKG combines semantic information with document topological information for the application of similar document retrieval. The CKG is constructed using the latent schema of the data, and then enriched with biomedical entity information extracted from the unstructured text of articles using scalable AWS technologies to form relations in the graph. Finally, we propose a document similarity engine that leverages low-dimensional graph embeddings from the CKG with semantic embeddings for similar article retrieval. Analysis demonstrates the quality of relationships in the CKG and shows that it can be used to uncover meaningful information in COVID-19 scientific articles. The CKG helps power www.cord19.aws and is publicly available.
We propose a distance supervised relation extraction approach for long-tailed, imbalanced data which is prevalent in real-world settings. Here, the challenge is to learn accurate few-shot models for classes existing at the tail of the class distribution, for which little data is available. Inspired by the rich semantic correlations between classes at the long tail and those at the head, we take advantage of the knowledge from data-rich classes at the head of the distribution to boost the performance of the data-poor classes at the tail. First, we propose to leverage implicit relational knowledge among class labels from knowledge graph embeddings and learn explicit relational knowledge using graph convolution networks. Second, we integrate that relational knowledge into relation extraction model by coarse-to-fine knowledge-aware attention mechanism. We demonstrate our results for a large-scale benchmark dataset which show that our approach significantly outperforms other baselines, especially for long-tail relations.
In this paper, we describe an embedding-based entity recommendation framework for Wikipedia that organizes Wikipedia into a collection of graphs layered on top of each other, learns complementary entity representations from their topology and content, and combines them with a lightweight learning-to-rank approach to recommend related entities on Wikipedia. Through offline and online evaluations, we show that the resulting embeddings and recommendations perform well in terms of quality and user engagement. Balancing simplicity and quality, this framework provides default entity recommendations for English and other languages in the Yahoo! Knowledge Graph, which Wikipedia is a core subset of.
Information Extraction (IE) from the tables present in scientific articles is challenging due to complicated tabular representations and complex embedded text. This paper presents TabLeX, a large-scale benchmark dataset comprising table images generated from scientific articles. TabLeX consists of two subsets, one for table structure extraction and the other for table content extraction. Each table image is accompanied by its corresponding LATEX source code. To facilitate the development of robust table IE tools, TabLeX contains images in different aspect ratios and in a variety of fonts. Our analysis sheds light on the shortcomings of current state-of-the-art table extraction models and shows that they fail on even simple table images. Towards the end, we experiment with a transformer-based existing baseline to report performance scores. In contrast to the static benchmarks, we plan to augment this dataset with more complex and diverse tables at regular intervals.
Open Information Extraction (OIE) is the task of extracting facts from sentences in the form of relations and their corresponding arguments in schema-free manner. Intrinsic performance of OIE systems is difficult to measure due to the incompleteness of existing OIE benchmarks: the ground truth extractions do not group all acceptable surface realizations of the same fact that can be extracted from a sentence. To measure performance of OIE systems more realistically, it is necessary to manually annotate complete facts (i.e., clusters of all acceptable surface realizations of the same fact) from input sentences. We propose AnnIE: an interactive annotation platform that facilitates such challenging annotation tasks and supports creation of complete fact-oriented OIE evaluation benchmarks. AnnIE is modular and flexible in order to support different use case scenarios (i.e., benchmarks covering different types of facts). We use AnnIE to build two complete OIE benchmarks: one with verb-mediated facts and another with facts encompassing named entities. Finally, we evaluate several OIE systems on our complete benchmarks created with AnnIE. Our results suggest that existing incomplete benchmarks are overly lenient, and that OIE systems are not as robust as previously reported. We publicly release AnnIE under non-restrictive license.
suggested questions
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
