An official website of the United States government
Chemical patents are an essential source of information about novel chemicals and chemical reactions. However, with the increasing volume of such patents, mining information about these chemicals and chemical reactions has become a time-intensive and laborious endeavor. In this study, we present a system to extract chemical reaction events from patents automatically. Our approach consists of two steps: 1) named entity recognition (NER)—the automatic identification of chemical reaction parameters from the corresponding text, and 2) event extraction (EE)—the automatic classifying and linking of entities based on their relationships to each other. For our NER system, we evaluate bidirectional long short-term memory (BiLSTM)-based and bidirectional encoder representations from transformer (BERT)-based methods. For our EE system, we evaluate BERT-based, convolutional neural network (CNN)-based, and rule-based methods. We evaluate our NER and EE components independently and as an end-to-end system, reporting the precision, recall, and F 1 score. Our results show that the BiLSTM-based method performed best at identifying the entities, and the CNN-based method performed best at extracting events.
more »
« less
Interpretability Analysis for Named Entity Recognition to Understand System Predictions and How They Can Improve
Abstract Named entity recognition systems achieve remarkable performance on domains such as English news. It is natural to ask: What are these models actually learning to achieve this? Are they merely memorizing the names themselves? Or are they capable of interpreting the text and inferring the correct entity type from the linguistic context? We examine these questions by contrasting the performance of several variants of architectures for named entity recognition, with some provided only representations of the context as features. We experiment with GloVe-based BiLSTM-CRF as well as BERT. We find that context does influence predictions, but the main factor driving high performance is learning the named tokens themselves. Furthermore, we find that BERT is not always better at recognizing predictive contexts compared to a BiLSTM-CRF model. We enlist human annotators to evaluate the feasibility of inferring entity types from context alone and find that humans are also mostly unable to infer entity types for the majority of examples on which the context-only system made errors. However, there is room for improvement: A system should be able to recognize any named entity in a predictive context correctly and our experiments indicate that current systems may be improved by such capability. Our human study also revealed that systems and humans do not always learn the same contextual clues, and context-only systems are sometimes correct even when humans fail to recognize the entity type from the context. Finally, we find that one issue contributing to model errors is the use of “entangled” representations that encode both contextual and local token information into a single vector, which can obscure clues. Our results suggest that designing models that explicitly operate over representations of local inputs and context, respectively, may in some cases improve performance. In light of these and related findings, we highlight directions for future work.
more »
« less
- Award ID(s):
- 1901117
- PAR ID:
- 10231019
- Date Published:
- Journal Name:
- Computational Linguistics
- Volume:
- 47
- Issue:
- 1
- ISSN:
- 0891-2017
- Page Range / eLocation ID:
- 117 to 140
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
null (Ed.)Named entity recognition (NER) is a fundamental task in the natural language processing (NLP) area. Recently, representation learning methods (e.g., character embedding and word embedding) have achieved promising recognition results. However, existing models only consider partial features derived from words or characters while failing to integrate semantic and syntactic information (e.g., capitalization, inter-word relations, keywords, lexical phrases, etc.) from multi-level perspectives. Intuitively, multi-level features can be helpful when recognizing named entities from complex sentences. In this study, we propose a novel framework called attention-based multi-level feature fusion (AMFF), which is used to capture the multi-level features from different perspectives to improve NER. Our model consists of four components to respectively capture the local character-level, global character-level, local word-level, and global word-level features, which are then fed into a BiLSTM-CRF network for the final sequence labeling. Extensive experimental results on four benchmark datasets show that our proposed model outperforms a set of state-of-the-art baselines.more » « less
-
Toponym detection in scientific papers is an open task and a key first step in place entity enrichment of documents. We examine three common neural architectures in NLP: 1) convolutional neural network, 2) multi-layer perceptron (both applied in a sliding window context) and 3) bidirectional LSTM and apply contextual and non-contextual word embedding layers to these models. We find that deep contextual word embeddings improve the performance of the bi-LSTM with CRF neural architecture achieving the best performance when multiple layers of deep contextual embeddings are concatenated. Our best performing model achieves an average F1 of 0.910 when evaluated on overlap macro exceeding previous state-of-the-art models in the toponym detection task.more » « less
-
Contextual word representations, typically trained on unstructured, unlabeled text, do not contain any explicit grounding to real world entities and are often unable to remember facts about those entities. We propose a general method to embed multiple knowledge bases (KBs) into large scale models, and thereby enhance their representations with structured, human-curated knowledge. For each KB, we first use an integrated entity linker to retrieve relevant entity embeddings, then update contextual word representations via a form of word-to-entity attention. In contrast to previous approaches, the entity linkers and self-supervised language modeling objective are jointly trained end-to-end in a multitask setting that combines a small amount of entity linking supervision with a large amount of raw text. After integrating WordNet and a subset of Wikipedia into BERT, the knowledge enhanced BERT (KnowBert) demonstrates improved perplexity, ability to recall facts as measured in a probing task and downstream performance on relationship extraction, entity typing, and word sense disambiguation. KnowBert’s runtime is comparable to BERT’s and it scales to large KBs.more » « less
-
Scientific literature presents a wellspring of cutting-edge knowledge for materials science, including valuable data (e.g., numerical data from experiment results, material properties and structure). These data are critical for accelerating materials discovery by data-driven machine learning (ML) methods. The challenge is, it is impossible for humans to manually extract and retain this knowledge due to the extensive and growing volume of publications.To this end, we explore a fine-tuned BERT model for extracting knowledge. Our preliminary results show that our fine-tuned Bert model reaches an f-score of 85% for the materials named entity recognition task. The paper covers background, related work, methodology including tuning parameters, and our overall performance evaluation. Our discussion offers insights into our results, and points to directions for next steps.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1162/coli_a_00397
