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"Information Extraction": models, code, and papers

Graph Convolution over Pruned Dependency Trees Improves Relation Extraction

Sep 26, 2018
Yuhao Zhang, Peng Qi, Christopher D. Manning

Dependency trees help relation extraction models capture long-range relations between words. However, existing dependency-based models either neglect crucial information (e.g., negation) by pruning the dependency trees too aggressively, or are computationally inefficient because it is difficult to parallelize over different tree structures. We propose an extension of graph convolutional networks that is tailored for relation extraction, which pools information over arbitrary dependency structures efficiently in parallel. To incorporate relevant information while maximally removing irrelevant content, we further apply a novel pruning strategy to the input trees by keeping words immediately around the shortest path between the two entities among which a relation might hold. The resulting model achieves state-of-the-art performance on the large-scale TACRED dataset, outperforming existing sequence and dependency-based neural models. We also show through detailed analysis that this model has complementary strengths to sequence models, and combining them further improves the state of the art.

* EMNLP 2018. Code available at: 

Plot2Spectra: an Automatic Spectra Extraction Tool

Jul 06, 2021
Weixin Jiang, Eric Schwenker, Trevor Spreadbury, Kai Li, Maria K. Y. Chan, Oliver Cossairt

Different types of spectroscopies, such as X-ray absorption near edge structure (XANES) and Raman spectroscopy, play a very important role in analyzing the characteristics of different materials. In scientific literature, XANES/Raman data are usually plotted in line graphs which is a visually appropriate way to represent the information when the end-user is a human reader. However, such graphs are not conducive to direct programmatic analysis due to the lack of automatic tools. In this paper, we develop a plot digitizer, named Plot2Spectra, to extract data points from spectroscopy graph images in an automatic fashion, which makes it possible for large scale data acquisition and analysis. Specifically, the plot digitizer is a two-stage framework. In the first axis alignment stage, we adopt an anchor-free detector to detect the plot region and then refine the detected bounding boxes with an edge-based constraint to locate the position of two axes. We also apply scene text detector to extract and interpret all tick information below the x-axis. In the second plot data extraction stage, we first employ semantic segmentation to separate pixels belonging to plot lines from the background, and from there, incorporate optical flow constraints to the plot line pixels to assign them to the appropriate line (data instance) they encode. Extensive experiments are conducted to validate the effectiveness of the proposed plot digitizer, which shows that such a tool could help accelerate the discovery and machine learning of materials properties.


DOM-LM: Learning Generalizable Representations for HTML Documents

Jan 25, 2022
Xiang Deng, Prashant Shiralkar, Colin Lockard, Binxuan Huang, Huan Sun

HTML documents are an important medium for disseminating information on the Web for human consumption. An HTML document presents information in multiple text formats including unstructured text, structured key-value pairs, and tables. Effective representation of these documents is essential for machine understanding to enable a wide range of applications, such as Question Answering, Web Search, and Personalization. Existing work has either represented these documents using visual features extracted by rendering them in a browser, which is typically computationally expensive, or has simply treated them as plain text documents, thereby failing to capture useful information presented in their HTML structure. We argue that the text and HTML structure together convey important semantics of the content and therefore warrant a special treatment for their representation learning. In this paper, we introduce a novel representation learning approach for web pages, dubbed DOM-LM, which addresses the limitations of existing approaches by encoding both text and DOM tree structure with a transformer-based encoder and learning generalizable representations for HTML documents via self-supervised pre-training. We evaluate DOM-LM on a variety of webpage understanding tasks, including Attribute Extraction, Open Information Extraction, and Question Answering. Our extensive experiments show that DOM-LM consistently outperforms all baselines designed for these tasks. In particular, DOM-LM demonstrates better generalization performance both in few-shot and zero-shot settings, making it attractive for making it suitable for real-world application settings with limited labeled data.


TabLeX: A Benchmark Dataset for Structure and Content Information Extraction from Scientific Tables

May 12, 2021
Harsh Desai, Pratik Kayal, Mayank Singh

Information Extraction (IE) from the tables present in scientific articles is challenging due to complicated tabular representations and complex embedded text. This paper presents TabLeX, a large-scale benchmark dataset comprising table images generated from scientific articles. TabLeX consists of two subsets, one for table structure extraction and the other for table content extraction. Each table image is accompanied by its corresponding LATEX source code. To facilitate the development of robust table IE tools, TabLeX contains images in different aspect ratios and in a variety of fonts. Our analysis sheds light on the shortcomings of current state-of-the-art table extraction models and shows that they fail on even simple table images. Towards the end, we experiment with a transformer-based existing baseline to report performance scores. In contrast to the static benchmarks, we plan to augment this dataset with more complex and diverse tables at regular intervals.


Distantly-Supervised Long-Tailed Relation Extraction Using Constraint Graphs

May 29, 2021
Tianming Liang, Yang Liu, Xiaoyan Liu, Gaurav Sharma, Maozu Guo

Label noise and long-tailed distributions are two major challenges in distantly supervised relation extraction. Recent studies have shown great progress on denoising, but pay little attention to the problem of long-tailed relations. In this paper, we introduce constraint graphs to model the dependencies between relation labels. On top of that, we further propose a novel constraint graph-based relation extraction framework(CGRE) to handle the two challenges simultaneously. CGRE employs graph convolution networks (GCNs) to propagate information from data-rich relation nodes to data-poor relation nodes, and thus boosts the representation learning of long-tailed relations. To further improve the noise immunity, a constraint-aware attention module is designed in CGRE to integrate the constraint information. Experimental results on a widely-used benchmark dataset indicate that our approach achieves significant improvements over the previous methods for both denoising and long-tailed relation extraction.


BI-RADS BERT & Using Section Tokenization to Understand Radiology Reports

Oct 14, 2021
Grey Kuling, Dr. Belinda Curpen, Anne L. Martel

Radiology reports are the main form of communication between radiologists and other clinicians, and contain important information for patient care. However in order to use this information for research it is necessary to convert the raw text into structured data suitable for analysis. Domain specific contextual word embeddings have been shown to achieve impressive accuracy at such natural language processing tasks in medicine. In this work we pre-trained a contextual embedding BERT model using breast radiology reports and developed a classifier that incorporated the embedding with auxiliary global textual features in order to perform a section tokenization task. This model achieved a 98% accuracy at segregating free text reports into sections of information outlined in the Breast Imaging Reporting and Data System (BI-RADS) lexicon, a significant improvement over the Classic BERT model without auxiliary information. We then evaluated whether using section tokenization improved the downstream extraction of the following fields: modality/procedure, previous cancer, menopausal status, purpose of exam, breast density and background parenchymal enhancement. Using the BERT model pre-trained on breast radiology reports combined with section tokenization resulted in an overall accuracy of 95.9% in field extraction. This is a 17% improvement compared to an overall accuracy of 78.9% for field extraction for models without section tokenization and with Classic BERT embeddings. Our work shows the strength of using BERT in radiology report analysis and the advantages of section tokenization in identifying key features of patient factors recorded in breast radiology reports.


Classification Algorithm of Speech Data of Parkinsons Disease Based on Convolution Sparse Kernel Transfer Learning with Optimal Kernel and Parallel Sample Feature Selection

Feb 10, 2020
Xiaoheng Zhang, Yongming Li, Pin Wang, Xiaoheng Tan, Yuchuan Liu

Labeled speech data from patients with Parkinsons disease (PD) are scarce, and the statistical distributions of training and test data differ significantly in the existing datasets. To solve these problems, dimensional reduction and sample augmentation must be considered. In this paper, a novel PD classification algorithm based on sparse kernel transfer learning combined with a parallel optimization of samples and features is proposed. Sparse transfer learning is used to extract effective structural information of PD speech features from public datasets as source domain data, and the fast ADDM iteration is improved to enhance the information extraction performance. To implement the parallel optimization, the potential relationships between samples and features are considered to obtain high-quality combined features. First, features are extracted from a specific public speech dataset to construct a feature dataset as the source domain. Then, the PD target domain, including the training and test datasets, is encoded by convolution sparse coding, which can extract more in-depth information. Next, parallel optimization is implemented. To further improve the classification performance, a convolution kernel optimization mechanism is designed. Using two representative public datasets and one self-constructed dataset, the experiments compare over thirty relevant algorithms. The results show that when taking the Sakar dataset, MaxLittle dataset and DNSH dataset as target domains, the proposed algorithm achieves obvious improvements in classification accuracy. The study also found large improvements in the algorithms in this paper compared with nontransfer learning approaches, demonstrating that transfer learning is both more effective and has a more acceptable time cost.

* 12 pages, 4 figures, 5 tables 

Automatically identifying, counting, and describing wild animals in camera-trap images with deep learning

Nov 15, 2017
Mohammed Sadegh Norouzzadeh, Anh Nguyen, Margaret Kosmala, Ali Swanson, Meredith Palmer, Craig Packer, Jeff Clune

Having accurate, detailed, and up-to-date information about the location and behavior of animals in the wild would revolutionize our ability to study and conserve ecosystems. We investigate the ability to automatically, accurately, and inexpensively collect such data, which could transform many fields of biology, ecology, and zoology into "big data" sciences. Motion sensor "camera traps" enable collecting wildlife pictures inexpensively, unobtrusively, and frequently. However, extracting information from these pictures remains an expensive, time-consuming, manual task. We demonstrate that such information can be automatically extracted by deep learning, a cutting-edge type of artificial intelligence. We train deep convolutional neural networks to identify, count, and describe the behaviors of 48 species in the 3.2-million-image Snapshot Serengeti dataset. Our deep neural networks automatically identify animals with over 93.8% accuracy, and we expect that number to improve rapidly in years to come. More importantly, if our system classifies only images it is confident about, our system can automate animal identification for 99.3% of the data while still performing at the same 96.6% accuracy as that of crowdsourced teams of human volunteers, saving more than 8.4 years (at 40 hours per week) of human labeling effort (i.e. over 17,000 hours) on this 3.2-million-image dataset. Those efficiency gains immediately highlight the importance of using deep neural networks to automate data extraction from camera-trap images. Our results suggest that this technology could enable the inexpensive, unobtrusive, high-volume, and even real-time collection of a wealth of information about vast numbers of animals in the wild.


Gextext: Disease Network Extraction from Biomedical Literature

Dec 17, 2019
Robert O'Shea

PURPOSE: We propose a fully unsupervised method to learn latent disease networks directly from unstructured biomedical text corpora. This method addresses current challenges in unsupervised knowledge extraction, such as the detection of long-range dependencies and requirements for large training corpora. METHODS: Let C be a corpus of n text chunks. Let V be a set of p disease terms occurring in the corpus. Let X indicate the occurrence of V in C. Gextext identifies disease similarities by positively correlated occurrence patterns. This information is combined to generate a graph on which geodesic distance describes dissimilarity. Diseasomes were learned by Gextext and GloVE on corpora of 100-1000 PubMed abstracts. Similarity matrix estimates were validated against biomedical semantic similarity metrics and gene profile similarity. RESULTS: Geodesic distance on Gextext-inferred diseasomes correlated inversely with external measures of semantic similarity. Gene profile similarity also correlated significant with proximity on the inferred graph. Gextext outperformed GloVE in our experiments. The information contained on the Gextext graph exceeded the explicit information content within the text. CONCLUSIONS: Gextext extracts latent relationships from unstructured text, enabling fully unsupervised modelling of diseasome graphs from PubMed abstracts.