skip to main content


Title: EZLearn: Exploiting Organic Supervision in Automated Data Annotation
Many real-world applications require automated data annotation, such as identifying tissue origins based on gene expressions and classifying images into semantic categories. Annotation classes are often numerous and subject to changes over time, and annotating examples has become the major bottleneck for supervised learning methods. In science and other high-value domains, large repositories of data samples are often available, together with two sources of organic supervision: a lexicon for the annotation classes, and text descriptions that accompany some data samples. Distant supervision has emerged as a promising paradigm for exploiting such indirect supervision by automatically annotating examples where the text description contains a class mention in the lexicon. However, due to linguistic variations and ambiguities, such training data is inherently noisy, which limits the accuracy in this approach. In this paper, we introduce an auxiliary natural language processing system for the text modality, and incorporate co-training to reduce noise and augment signal in distant supervision. Without using any manually labeled data, our EZLearn system learned to accurately annotate data samples in functional genomics and scientific figure comprehension, substantially outperforming state-of-the-art supervised methods trained on tens of thousands of annotated examples.  more » « less
Award ID(s):
1740996
NSF-PAR ID:
10074152
Author(s) / Creator(s):
; ;
Date Published:
Journal Name:
Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. null (Ed.)
    Supervised deep learning methods have achieved state-of-the-art performance on the task of named entity recognition (NER). However, such methods suffer from high cost and low efficiency in training data annotation, leading to highly specialized NER models that cannot be easily adapted to new domains. Recently, distant supervision has been applied to replace human annotation, thanks to the fast development of domain-specific knowledge bases. However, the generated noisy labels pose significant challenges in learning effective neural models with distant supervision. We propose PATNER, a distantly supervised NER model that effectively deals with noisy distant supervision from domain-specific dictionaries. PATNER does not require human-annotated training data but only relies on unlabeled data and incomplete domain-specific dictionaries for distant supervision. It incorporates the distant labeling uncertainty into the neural model training to enhance distant supervision. We go beyond the traditional sequence labeling framework and propose a more effective fuzzy neural model using the tie-or-break tagging scheme for the NER task. Extensive experiments on three benchmark datasets in two domains demonstrate the power of PATNER. Case studies on two additional real-world datasets demonstrate that PATNER improves the distant NER performance in both entity boundary detection and entity type recognition. The results show a great promise in supporting high quality named entity recognition with domain-specific dictionaries on a wide variety of entity types. 
    more » « less
  2. 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
  3. 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
  4. Deep neural networks are gaining increasing popularity for the classic text classification task, due to their strong expressive power and less requirement for feature engineering. Despite such attractiveness, neural text classification models suffer from the lack of training data in many real-world applications. Although many semisupervised and weakly-supervised text classification models exist, they cannot be easily applied to deep neural models and meanwhile support limited supervision types. In this paper, we propose a weakly-supervised method that addresses the lack of training data in neural text classification. Our method consists of two modules: (1) a pseudo-document generator that leverages seed information to generate pseudo-labeled documents for model pre-training, and (2) a self-training module that bootstraps on real unlabeled data for model refinement. Our method has the flexibility to handle different types of weak supervision and can be easily integrated into existing deep neural models for text classification. We have performed extensive experiments on three real-world datasets from different domains. The results demonstrate that our proposed method achieves inspiring performance without requiring excessive training data and outperforms baseline methods significantly. 
    more » « less
  5. Recognizing entity synonyms from text has become a crucial task in many entity-leveraging applications. However, discovering entity synonyms from domain-specific text corpora (e.g., news articles, scientific papers) is rather challenging. Current systems take an entity name string as input to find out other names that are synonymous, ignoring the fact that often times a name string can refer to multiple entities (e.g., “apple” could refer to both Apple Inc and the fruit apple). Moreover, most existing methods require training data manually created by domain experts to construct supervised learning systems. In this paper, we study the problem of automatic synonym discovery with knowledge bases, that is, identifying synonyms for knowledge base entities in a given domain-specific corpus. The manually-curated synonyms for each entity stored in a knowledge base not only form a set of name strings to disambiguate the meaning for each other, but also can serve as “distant” supervision to help determine important features for the task. We propose a novel framework, called DPE, to integrate two kinds of mutually complementing signals for synonym discovery, i.e., distributional features based on corpus-level statistics and textual patterns based on local contexts. In particular, DPE jointly optimizes the two kinds of signals in conjunction with distant supervision, so that they can mutually enhance each other in the training stage. At the inference stage, both signals will be utilized to discover synonyms for the given entities. Experimental results prove the effectiveness of the proposed framework. 
    more » « less