An official website of the United States government
Machine learning on graph structured data has attracted much research interest due to its ubiquity in real world data. However, how to efficiently represent graph data in a general way is still an open problem. Traditional methods use handcraft graph features in a tabular form but suffer from the defects of domain expertise requirement and information loss. Graph representation learning overcomes these defects by automatically learning the continuous representations from graph structures, but they require abundant training labels, which are often hard to fulfill for graph-level prediction problems. In this work, we demonstrate that, if available, the domain expertise used for designing handcraft graph features can improve the graph-level representation learning when training labels are scarce. Specifically, we proposed a multi-task knowledge distillation method. By incorporating network-theory-based graph metrics as auxiliary tasks, we show on both synthetic and real datasets that the proposed multi-task learning method can improve the prediction performance of the original learning task, especially when the training data size is small.
more »
« less
ReactIE: Enhancing Chemical Reaction Extraction with Weak Supervision
Structured chemical reaction information plays a vital role for chemists engaged in laboratory work and advanced endeavors such as computer-aided drug design. Despite the importance of extracting structured reactions from scientific literature, data annotation for this purpose is cost-prohibitive due to the significant labor required from domain experts. Consequently, the scarcity of sufficient training data poses an obstacle to the progress of related models in this domain. In this paper, we propose REACTIE, which combines two weakly supervised approaches for pre-training. Our method utilizes frequent patterns within the text as linguistic cues to identify specific characteristics of chemical reactions. Additionally, we adopt synthetic data from patent records as distant supervision to incorporate domain knowledge into the model. Experiments demonstrate that REACTIE achieves substantial improvements and outperforms all existing baselines.
more »
« less
- PAR ID:
- 10467005
- Publisher / Repository:
- Association for Computational Linguistics
- Date Published:
- Page Range / eLocation ID:
- 12120 to 12130
- Subject(s) / Keyword(s):
- ReactIE, information extraction, weakly supervised approach, machine learning, text mining, scientific literature
- Format(s):
- Medium: X
- Location:
- Toronto, Canada
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Scientific literature analysis needs fine-grained named entity recognition (NER) to provide a wide range of information for scientific discovery. For example, chemistry research needs to study dozens to hundreds of distinct, fine-grained entity types, making consistent and accurate annotation difficult even for crowds of domain experts. On the other hand, domain-specific ontologies and knowledge bases (KBs) can be easily accessed, constructed, or integrated, which makes distant supervision realistic for fine-grained chemistry NER. In distant supervision, training labels are generated by matching mentions in a document with the concepts in the knowledge bases (KBs). However, this kind of KB-matching suffers from two major challenges: incomplete annotation and noisy annotation. We propose ChemNER, an ontology-guided, distantly-supervised method for fine-grained chemistry NER to tackle these challenges. It leverages the chemistry type ontology structure to generate distant labels with novel methods of flexible KB-matching and ontology-guided multi-type disambiguation. It significantly improves the distant label generation for the subsequent sequence labeling model training. We also provide an expert-labeled, chemistry NER dataset with 62 fine-grained chemistry types (e.g., chemical compounds and chemical reactions). Experimental results show that ChemNER is highly effective, outperforming substantially the state-of-the-art NER methods (with .25 absolute F1 score improvement).more » « less
-
Developing methods of automated inference that are able to provide users with compelling human-readable justifications for why the answer to a question is correct is critical for domains such as science and medicine, where user trust and detecting costly errors are limiting factors to adoption. One of the central barriers to training question answering models on explainable inference tasks is the lack of gold explanations to serve as training data. In this paper we present a corpus of explanations for standardized science exams, a recent challenge task for question answering. We manually construct a corpus of detailed explanations for nearly all publicly available standardized elementary science question (approximately 1,680 3 rd through 5 th grade questions) and represent these as “explanation graphs” - sets of lexically overlapping sentences that describe how to arrive at the correct answer to a question through a combination of domain and world knowledge. We also provide an explanation-centered tablestore, a collection of semi-structured tables that contain the knowledge to construct these elementary science explanations. Together, these two knowledge resources map out a substantial portion of the knowledge required for answering and explaining elementary science exams, and provide both structured and free-text training data for the explainable inference task.more » « less
-
A Natural Language Interface (NLI) enables the use of human languages to interact with computer systems, including smart phones and robots. Compared to other types of interfaces, such as command line interfaces (CLIs) or graphical user interfaces (GUIs), NLIs stand to enable more people to have access to functionality behind databases or APIs as they only require knowledge of natural languages. Many NLI applications involve structured data for the domain (e.g., applications such as hotel booking, product search, and factual question answering.) Thus, to fully process user questions, in addition to natural language comprehension, understanding of structured data is also crucial for the model. In this paper, we study neural network methods for building Natural Language Interfaces (NLIs) with a focus on learning structure data representations that can generalize to novel data sources and schemata not seen at training time. Specifically, we review two tasks related to natural language interfaces: i) semantic parsing where we focus on text-to-SQL for database access, and ii) task-oriented dialog systems for API access. We survey representative methods for text-to-SQL and task-oriented dialog tasks, focusing on representing and incorporating structured data. Lastly, we present two of our original studies on structured data representation methods for NLIs to enable access to i) databases, and ii) visualization APIs.more » « less
-
The lack of publicly available, large, and unbiased datasets is a key bottleneck for the application of machine learning (ML) methods in synthetic chemistry. Data from electronic laboratory notebooks (ELNs) could provide less biased, large datasets, but no such datasets have been made publicly available. The first real-world dataset from the ELNs of a large pharmaceutical company is disclosed and its relationship to high-throughput experimentation (HTE) datasets is described. For chemical yield predictions, a key task in chemical synthesis, an attributed graph neural network (AGNN) performs as well as or better than the best previous models on two HTE datasets for the Suzuki–Miyaura and Buchwald–Hartwig reactions. However, training the AGNN on an ELN dataset does not lead to a predictive model. The implications of using ELN data for training ML-based models are discussed in the context of yield predictions.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Conference Paper:
- https://doi.org/10.18653/v1/2023.findings-acl.767
