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.
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On the Potential of Lexico-logical Alignments for Semantic Parsing to SQL Queries
Large-scale semantic parsing datasets annotated with logical forms have enabled major advances in supervised approaches. But can richer supervision help even more? To explore the utility of fine-grained, lexical-level supervision, we introduce SQUALL, a dataset that enriches 11,276 WIKITABLEQUESTIONS English-language questions with manually created SQL equivalents plus alignments between SQL and question fragments. Our annotation enables new training possibilities for encoderdecoder models, including approaches from machine translation previously precluded by the absence of alignments. We propose and test two methods: (1) supervised attention; (2) adopting an auxiliary objective of disambiguating references in the input queries to table columns. In 5-fold cross validation, these strategies improve over strong baselines by 4.4% execution accuracy. Oracle experiments suggest that annotated alignments can support further accuracy gains of up to 23.9%.
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- PAR ID:
- 10212075
- Date Published:
- Journal Name:
- Findings of the Association for Computational Linguistics: EMNLP 2020
- Page Range / eLocation ID:
- 1849 to 1864
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract Accurate alignment of transcribed RNA to reference genomes is a critical step in the analysis of gene expression, which in turn has broad applications in biomedical research and in the basic sciences. We reveal that widely used splice-aware aligners, such as STAR and HISAT2, can introduce erroneous spliced alignments between repeated sequences, leading to the inclusion of falsely spliced transcripts in RNA-seq experiments. In some cases, the ‘phantom’ introns resulting from these errors make their way into widely-used genome annotation databases. To address this issue, we present EASTR (Emending Alignments of Spliced Transcript Reads), a software tool that detects and removes falsely spliced alignments or transcripts from alignment and annotation files. EASTR improves the accuracy of spliced alignments across diverse species, including human, maize, and
Arabidopsis thaliana , by detecting sequence similarity between intron-flanking regions. We demonstrate that applying EASTR before transcript assembly substantially reduces false positive introns, exons, and transcripts, improving the overall accuracy of assembled transcripts. Additionally, we show that EASTR’s application to reference annotation databases can detect and correct likely cases of mis-annotated transcripts.
- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Conference Paper:
- https://doi.org/10.18653/v1/2020.findings-emnlp.167
