A study on developing novel methods for relation extraction

Relation Extraction (RE) is a task of Natural Language Processing (NLP) to detect and classify the relations between two entities. Relation extraction in the biomedical and scientific literature domain is challenging as text can contain multiple pairs of entities in the same instance. During the course of this research, we developed an RE framework (RelEx), which consists of five main RE paradigms: rule-based, machine learning-based, Convolutional Neural Network (CNN)-based, Bidirectional Encoder Representations from Transformers (BERT)-based, and Graph Convolutional Networks (GCNs)-based approaches. RelEx\u27s rule-based approach uses co-location information of the entities to determine whether a relation exists between a selected entity and the other entities. RelEx\u27s machine learning-based approach consists of traditional feature representations into traditional machine learning algorithms. RelEx\u27s CNN-based approach consists of three CNN architectures: Segment-CNN, single-label Sentence-CNN, and multi-label Sentence-CNN. RelEx\u27s BERT-based approach utilizes BERT\u27s contextualized word embeddings into a feed-forward neural network. Finally, RelEx\u27s GCN-based approach consists of two GCN-based architectures: GCN-Vanilla, GCN-BERT. We evaluated variations of these approaches in two different domains across four distinct relation types. Overall our findings showed that the rule-based approach is applicable for data with fewer instances in the training data. In contrast, the CNN-based, BERT-based, and GCN-based approaches perform better with labeled data with many training instances. These approaches automatically identify patterns in the data efficiently, whereas rule-based approaches require expert knowledge to generate rules. The CNN-based, BERT-based approaches capture the local contextual information within a sentence or document by embedding both semantic and syntactic information in a learned representation. However, their ability to capture the long-range dependency global information in a text is limited. GCN-based approaches capture the global association information by performing convolution operations on neighbor nodes in a graph and incorporating information from neighbors. Combining GCN with BERT integrates the local contextual and global association information of the words and generates better representations for the words

STIXnet: A Novel and Modular Solution for Extracting All STIX Objects in CTI Reports

The automatic extraction of information from Cyber Threat Intelligence (CTI) reports is crucial in risk management. The increased frequency of the publications of these reports has led researchers to develop new systems for automatically recovering different types of entities and relations from textual data. Most state-of-the-art models leverage Natural Language Processing (NLP) techniques, which perform greatly in extracting a few types of entities at a time but cannot detect heterogeneous data or their relations. Furthermore, several paradigms, such as STIX, have become de facto standards in the CTI community and dictate a formal categorization of different entities and relations to enable organizations to share data consistently. This paper presents STIXnet, the first solution for the automated extraction of all STIX entities and relationships in CTI reports. Through the use of NLP techniques and an interactive Knowledge Base (KB) of entities, our approach obtains F1 scores comparable to state-of-the-art models for entity extraction (0.916) and relation extraction (0.724) while considering significantly more types of entities and relations. Moreover, STIXnet constitutes a modular and extensible framework that manages and coordinates different modules to merge their contributions uniquely and exhaustively. With our approach, researchers and organizations can extend their Information Extraction (IE) capabilities by integrating the efforts of several techniques without needing to develop new tools from scratch.Comment: 11 pages, 3 figure

Classifying Relations using Recurrent Neural Network with Ontological-Concept Embedding

Relation extraction and classification represents a fundamental and challenging aspect of Natural Language Processing (NLP) research which depends on other tasks such as entity detection and word sense disambiguation. Traditional relation extraction methods based on pattern-matching using regular expressions grammars and lexico-syntactic pattern rules suffer from several drawbacks including the labor involved in handcrafting and maintaining large number of rules that are difficult to reuse. Current research has focused on using Neural Networks to help improve the accuracy of relation extraction tasks using a specific type of Recurrent Neural Network (RNN). A promising approach for relation classification uses an RNN that incorporates an ontology-based concept embedding layer in addition to word embeddings. This dissertation presents several improvements to this approach by addressing its main limitations. First, several different types of semantic relationships between concepts are incorporated into the model; prior work has only considered is-a hierarchical relationships. Secondly, a significantly larger vocabulary of concepts is used. Thirdly, an improved method for concept matching was devised. The results of adding these improvements to two state-of-the-art baseline models demonstrated an improvement to accuracy when evaluated on benchmark data used in prior studies

Deep Neural Architectures for End-to-End Relation Extraction

The rapid pace of scientific and technological advancements has led to a meteoric growth in knowledge, as evidenced by a sharp increase in the number of scholarly publications in recent years. PubMed, for example, archives more than 30 million biomedical articles across various domains and covers a wide range of topics including medicine, pharmacy, biology, and healthcare. Social media and digital journalism have similarly experienced their own accelerated growth in the age of big data. Hence, there is a compelling need for ways to organize and distill the vast, fragmented body of information (often unstructured in the form of natural human language) so that it can be assimilated, reasoned about, and ultimately harnessed. Relation extraction is an important natural language task toward that end. In relation extraction, semantic relationships are extracted from natural human language in the form of (subject, object, predicate) triples such that subject and object are mentions of discrete concepts and predicate indicates the type of relation between them. The difficulty of relation extraction becomes clear when we consider the myriad of ways the same relation can be expressed in natural language. Much of the current works in relation extraction assume that entities are known at extraction time, thus treating entity recognition as an entirely separate and independent task. However, recent studies have shown that entity recognition and relation extraction, when modeled together as interdependent tasks, can lead to overall improvements in extraction accuracy. When modeled in such a manner, the task is referred to as end-to-end relation extraction. In this work, we present four studies that introduce incrementally sophisticated architectures designed to tackle the task of end-to-end relation extraction. In the first study, we present a pipeline approach for extracting protein-protein interactions as affected by particular mutations. The pipeline system makes use of recurrent neural networks for protein detection, lexicons for gene normalization, and convolutional neural networks for relation extraction. In the second study, we show that a multi-task learning framework, with parameter sharing, can achieve state-of-the-art results for drug-drug interaction extraction. At its core, the model uses graph convolutions, with a novel attention-gating mechanism, over dependency parse trees. In the third study, we present a more efficient and general-purpose end-to-end neural architecture designed around the idea of the table-filling paradigm; for an input sentence of length n, all entities and relations are extracted in a single pass of the network in an indirect fashion by populating the cells of a corresponding n by n table using metric-based features. We show that this approach excels in both the general English and biomedical domains with extraction times that are up to an order of magnitude faster compared to the prior best. In the fourth and last study, we present an architecture for relation extraction that, in addition to being end-to-end, is able to handle cross-sentence and N-ary relations. Overall, our work contributes to the advancement of modern information extraction by exploring end-to-end solutions that are fast, accurate, and generalizable to many high-value domains