Donghong Ji

Bio: Donghong Ji is an academic researcher from Wuhan University. The author has contributed to research in topics: Computer science & Relationship extraction. The author has an hindex of 26, co-authored 132 publications receiving 2837 citations. Previous affiliations of Donghong Ji include Institute for Infocomm Research Singapore.

The CHEMDNER corpus of chemicals and drugs and its annotation principles.

Abstract: The automatic extraction of chemical information from text requires the recognition of chemical entity mentions as one of its key steps. When developing supervised named entity recognition (NER) systems, the availability of a large, manually annotated text corpus is desirable. Furthermore, large corpora permit the robust evaluation and comparison of different approaches that detect chemicals in documents. We present the CHEMDNER corpus, a collection of 10,000 PubMed abstracts that contain a total of 84,355 chemical entity mentions labeled manually by expert chemistry literature curators, following annotation guidelines specifically defined for this task. The abstracts of the CHEMDNER corpus were selected to be representative for all major chemical disciplines. Each of the chemical entity mentions was manually labeled according to its structure-associated chemical entity mention (SACEM) class: abbreviation, family, formula, identifier, multiple, systematic and trivial. The difficulty and consistency of tagging chemicals in text was measured using an agreement study between annotators, obtaining a percentage agreement of 91. For a subset of the CHEMDNER corpus (the test set of 3,000 abstracts) we provide not only the Gold Standard manual annotations, but also mentions automatically detected by the 26 teams that participated in the BioCreative IV CHEMDNER chemical mention recognition task. In addition, we release the CHEMDNER silver standard corpus of automatically extracted mentions from 17,000 randomly selected PubMed abstracts. A version of the CHEMDNER corpus in the BioC format has been generated as well. We propose a standard for required minimum information about entity annotations for the construction of domain specific corpora on chemical and drug entities. The CHEMDNER corpus and annotation guidelines are available at: http://www.biocreative.org/resources/biocreative-iv/chemdner-corpus/

A neural joint model for entity and relation extraction from biomedical text

Abstract: Extracting biomedical entities and their relations from text has important applications on biomedical research. Previous work primarily utilized feature-based pipeline models to process this task. Many efforts need to be made on feature engineering when feature-based models are employed. Moreover, pipeline models may suffer error propagation and are not able to utilize the interactions between subtasks. Therefore, we propose a neural joint model to extract biomedical entities as well as their relations simultaneously, and it can alleviate the problems above. Our model was evaluated on two tasks, i.e., the task of extracting adverse drug events between drug and disease entities, and the task of extracting resident relations between bacteria and location entities. Compared with the state-of-the-art systems in these tasks, our model improved the F1 scores of the first task by 5.1% in entity recognition and 8.0% in relation extraction, and that of the second task by 9.2% in relation extraction. The proposed model achieves competitive performances with less work on feature engineering. We demonstrate that the model based on neural networks is effective for biomedical entity and relation extraction. In addition, parameter sharing is an alternative method for neural models to jointly process this task. Our work can facilitate the research on biomedical text mining.

Tree Kernel-Based Relation Extraction with Context-Sensitive Structured Parse Tree Information

Abstract: This paper proposes a tree kernel with contextsensitive structured parse tree information for relation extraction. It resolves two critical problems in previous tree kernels for relation extraction in two ways. First, it automatically determines a d ynamic context-sensitive tree span for relation extraction by extending the widely -used Shortest Path-enclosed Tree (SPT) to include necessary context information outside SPT. Second, it pr oposes a context -sensitive convolution tree kernel, which enumerates both context-free and contextsensitive sub-trees by consid ering their ancestor node paths as their contexts. Moreover, this paper evaluates the complementary nature between our tree kernel and a state -of-the-art linear kernel. Evaluation on the ACE RDC corpora shows that our dynamic context-sensitive tree span is much more suitable for relation extraction than SPT and our tree kernel outperforms the state-of-the-art Collins and Duffy’s convolution tree kernel. It also shows that our tree kernel achieves much better performance than the state-of-the-art linear kernels . Finally, it shows that feature-based and tree kernel-based methods much complement each other and the composite kernel can well integrate both flat and structured features.

Dependency Graph Enhanced Dual-transformer Structure for Aspect-based Sentiment Classification.

Abstract: Aspect-based sentiment classification is a popular task aimed at identifying the corresponding emotion of a specific aspect. One sentence may contain various sentiments for different aspects. Many sophisticated methods such as attention mechanism and Convolutional Neural Networks (CNN) have been widely employed for handling this challenge. Recently, semantic dependency tree implemented by Graph Convolutional Networks (GCN) is introduced to describe the inner connection between aspects and the associated emotion words. But the improvement is limited due to the noise and instability of dependency trees. To this end, we propose a dependency graph enhanced dual-transformer network (named DGEDT) by jointly considering the flat representations learnt from Transformer and graph-based representations learnt from the corresponding dependency graph in an iterative interaction manner. Specifically, a dual-transformer structure is devised in DGEDT to support mutual reinforcement between the flat representation learning and graph-based representation learning. The idea is to allow the dependency graph to guide the representation learning of the transformer encoder and vice versa. The results on five datasets demonstrate that the proposed DGEDT outperforms all state-of-the-art alternatives with a large margin.

Visual Genome: Connecting Language and Vision Using Crowdsourced Dense Image Annotations

Abstract: Despite progress in perceptual tasks such as image classification, computers still perform poorly on cognitive tasks such as image description and question answering. Cognition is core to tasks that involve not just recognizing, but reasoning about our visual world. However, models used to tackle the rich content in images for cognitive tasks are still being trained using the same datasets designed for perceptual tasks. To achieve success at cognitive tasks, models need to understand the interactions and relationships between objects in an image. When asked "What vehicle is the person riding?", computers will need to identify the objects in an image as well as the relationships riding(man, carriage) and pulling(horse, carriage) to answer correctly that "the person is riding a horse-drawn carriage." In this paper, we present the Visual Genome dataset to enable the modeling of such relationships. We collect dense annotations of objects, attributes, and relationships within each image to learn these models. Specifically, our dataset contains over 108K images where each image has an average of $$35$$35 objects, $$26$$26 attributes, and $$21$$21 pairwise relationships between objects. We canonicalize the objects, attributes, relationships, and noun phrases in region descriptions and questions answer pairs to WordNet synsets. Together, these annotations represent the densest and largest dataset of image descriptions, objects, attributes, relationships, and question answer pairs.

Distant supervision for relation extraction without labeled data

Abstract: Modern models of relation extraction for tasks like ACE are based on supervised learning of relations from small hand-labeled corpora. We investigate an alternative paradigm that does not require labeled corpora, avoiding the domain dependence of ACE-style algorithms, and allowing the use of corpora of any size. Our experiments use Freebase, a large semantic database of several thousand relations, to provide distant supervision. For each pair of entities that appears in some Freebase relation, we find all sentences containing those entities in a large unlabeled corpus and extract textual features to train a relation classifier. Our algorithm combines the advantages of supervised IE (combining 400,000 noisy pattern features in a probabilistic classifier) and unsupervised IE (extracting large numbers of relations from large corpora of any domain). Our model is able to extract 10,000 instances of 102 relations at a precision of 67.6%. We also analyze feature performance, showing that syntactic parse features are particularly helpful for relations that are ambiguous or lexically distant in their expression.

BioBERT: a pre-trained biomedical language representation model for biomedical text mining.

Abstract: Motivation Biomedical text mining is becoming increasingly important as the number of biomedical documents rapidly grows. With the progress in natural language processing (NLP), extracting valuable information from biomedical literature has gained popularity among researchers, and deep learning has boosted the development of effective biomedical text mining models. However, directly applying the advancements in NLP to biomedical text mining often yields unsatisfactory results due to a word distribution shift from general domain corpora to biomedical corpora. In this article, we investigate how the recently introduced pre-trained language model BERT can be adapted for biomedical corpora. Results We introduce BioBERT (Bidirectional Encoder Representations from Transformers for Biomedical Text Mining), which is a domain-specific language representation model pre-trained on large-scale biomedical corpora. With almost the same architecture across tasks, BioBERT largely outperforms BERT and previous state-of-the-art models in a variety of biomedical text mining tasks when pre-trained on biomedical corpora. While BERT obtains performance comparable to that of previous state-of-the-art models, BioBERT significantly outperforms them on the following three representative biomedical text mining tasks: biomedical named entity recognition (0.62% F1 score improvement), biomedical relation extraction (2.80% F1 score improvement) and biomedical question answering (12.24% MRR improvement). Our analysis results show that pre-training BERT on biomedical corpora helps it to understand complex biomedical texts. Availability and implementation We make the pre-trained weights of BioBERT freely available at https://github.com/naver/biobert-pretrained, and the source code for fine-tuning BioBERT available at https://github.com/dmis-lab/biobert.

Word sense disambiguation: A survey

Abstract: Word sense disambiguation (WSD) is the ability to identify the meaning of words in context in a computational manner. WSD is considered an AI-complete problem, that is, a task whose solution is at least as hard as the most difficult problems in artificial intelligence. We introduce the reader to the motivations for solving the ambiguity of words and provide a description of the task. We overview supervised, unsupervised, and knowledge-based approaches. The assessment of WSD systems is discussed in the context of the Senseval/Semeval campaigns, aiming at the objective evaluation of systems participating in several different disambiguation tasks. Finally, applications, open problems, and future directions are discussed.