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"Information Extraction": models, code, and papers

Comprehend Medical: a Named Entity Recognition and Relationship Extraction Web Service

Oct 15, 2019
Parminder Bhatia, Busra Celikkaya, Mohammed Khalilia, Selvan Senthivel

Comprehend Medical is a stateless and Health Insurance Portability and Accountability Act (HIPAA) eligible Named Entity Recognition (NER) and Relationship Extraction (RE) service launched under Amazon Web Services (AWS) trained using state-of-the-art deep learning models. Contrary to many existing open source tools, Comprehend Medical is scalable and does not require steep learning curve, dependencies, pipeline configurations, or installations. Currently, Comprehend Medical performs NER in five medical categories: Anatomy, Medical Condition, Medications, Protected Health Information (PHI) and Treatment, Test and Procedure (TTP). Additionally, the service provides relationship extraction for the detected entities as well as contextual information such as negation and temporality in the form of traits. Comprehend Medical provides two Application Programming Interfaces (API): 1) the NERe API which returns all the extracted named entities, their traits and the relationships between them and 2) the PHId API which returns just the protected health information contained in the text. Furthermore, Comprehend Medical is accessible through AWS Console, Java and Python Software Development Kit (SDK), making it easier for non-developers and developers to use.

* ICMLA 2019. $\copyright$ 2019 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses in any current or future media including reprinting/republishing this material for advertising, promotional purposes, creating new collective works, for resale or redistribution to servers or lists, reuse of any copyrighted component of this work in other works. arXiv admin note: text overlap with arXiv:1812.05270 

Speaker activity driven neural speech extraction

Feb 09, 2021
Marc Delcroix, Katerina Zmolikova, Tsubasa Ochiai, Keisuke Kinoshita, Tomohiro Nakatani

Target speech extraction, which extracts the speech of a target speaker in a mixture given auxiliary speaker clues, has recently received increased interest. Various clues have been investigated such as pre-recorded enrollment utterances, direction information, or video of the target speaker. In this paper, we explore the use of speaker activity information as an auxiliary clue for single-channel neural network-based speech extraction. We propose a speaker activity driven speech extraction neural network (ADEnet) and show that it can achieve performance levels competitive with enrollment-based approaches, without the need for pre-recordings. We further demonstrate the potential of the proposed approach for processing meeting-like recordings, where the speaker activity is obtained from a diarization system. We show that this simple yet practical approach can successfully extract speakers after diarization, which results in improved ASR performance, especially in high overlapping conditions, with a relative word error rate reduction of up to 25%.

* To appear in ICASSP 2021 

Improving Distantly-Supervised Relation Extraction through BERT-based Label & Instance Embeddings

Feb 01, 2021
Despina Christou, Grigorios Tsoumakas

Distantly-supervised relation extraction (RE) is an effective method to scale RE to large corpora but suffers from noisy labels. Existing approaches try to alleviate noise through multi-instance learning and by providing additional information, but manage to recognize mainly the top frequent relations, neglecting those in the long-tail. We propose REDSandT (Relation Extraction with Distant Supervision and Transformers), a novel distantly-supervised transformer-based RE method, that manages to capture a wider set of relations through highly informative instance and label embeddings for RE, by exploiting BERT's pre-trained model, and the relationship between labels and entities, respectively. We guide REDSandT to focus solely on relational tokens by fine-tuning BERT on a structured input, including the sub-tree connecting an entity pair and the entities' types. Using the extracted informative vectors, we shape label embeddings, which we also use as attention mechanism over instances to further reduce noise. Finally, we represent sentences by concatenating relation and instance embeddings. Experiments in the NYT-10 dataset show that REDSandT captures a broader set of relations with higher confidence, achieving state-of-the-art AUC (0.424).

* 10 pages, 4 figures 

Training privacy-preserving video analytics pipelines by suppressing features that reveal information about private attributes

Mar 05, 2022
Chau Yi Li, Andrea Cavallaro

Deep neural networks are increasingly deployed for scene analytics, including to evaluate the attention and reaction of people exposed to out-of-home advertisements. However, the features extracted by a deep neural network that was trained to predict a specific, consensual attribute (e.g. emotion) may also encode and thus reveal information about private, protected attributes (e.g. age or gender). In this work, we focus on such leakage of private information at inference time. We consider an adversary with access to the features extracted by the layers of a deployed neural network and use these features to predict private attributes. To prevent the success of such an attack, we modify the training of the network using a confusion loss that encourages the extraction of features that make it difficult for the adversary to accurately predict private attributes. We validate this training approach on image-based tasks using a publicly available dataset. Results show that, compared to the original network, the proposed PrivateNet can reduce the leakage of private information of a state-of-the-art emotion recognition classifier by 2.88% for gender and by 13.06% for age group, with a minimal effect on task accuracy.


Biomedical Information Extraction for Disease Gene Prioritization

Nov 12, 2020
Jupinder Parmar, William Koehler, Martin Bringmann, Katharina Sophia Volz, Berk Kapicioglu

We introduce a biomedical information extraction (IE) pipeline that extracts biological relationships from text and demonstrate that its components, such as named entity recognition (NER) and relation extraction (RE), outperform state-of-the-art in BioNLP. We apply it to tens of millions of PubMed abstracts to extract protein-protein interactions (PPIs) and augment these extractions to a biomedical knowledge graph that already contains PPIs extracted from STRING, the leading structured PPI database. We show that, despite already containing PPIs from an established structured source, augmenting our own IE-based extractions to the graph allows us to predict novel disease-gene associations with a 20% relative increase in [email protected], an important step towards developing drug targets for uncured diseases.

* 4th Knowledge Representation and Reasoning Meets Machine Learning Workshop (KR2ML), at NeurIPS 2020 

Multimodal Approach for Metadata Extraction from German Scientific Publications

Nov 10, 2021
Azeddine Bouabdallah, Jorge Gavilan, Jennifer Gerbl, Prayuth Patumcharoenpol

Nowadays, metadata information is often given by the authors themselves upon submission. However, a significant part of already existing research papers have missing or incomplete metadata information. German scientific papers come in a large variety of layouts which makes the extraction of metadata a non-trivial task that requires a precise way to classify the metadata extracted from the documents. In this paper, we propose a multimodal deep learning approach for metadata extraction from scientific papers in the German language. We consider multiple types of input data by combining natural language processing and image vision processing. This model aims to increase the overall accuracy of metadata extraction compared to other state-of-the-art approaches. It enables the utilization of both spatial and contextual features in order to achieve a more reliable extraction. Our model for this approach was trained on a dataset consisting of around 8800 documents and is able to obtain an overall F1-score of 0.923.

* 8 pages, 5 figures, 4 tables 

RadGraph: Extracting Clinical Entities and Relations from Radiology Reports

Jun 28, 2021
Saahil Jain, Ashwin Agrawal, Adriel Saporta, Steven QH Truong, Du Nguyen Duong, Tan Bui, Pierre Chambon, Yuhao Zhang, Matthew P. Lungren, Andrew Y. Ng, Curtis P. Langlotz, Pranav Rajpurkar

Extracting structured clinical information from free-text radiology reports can enable the use of radiology report information for a variety of critical healthcare applications. In our work, we present RadGraph, a dataset of entities and relations in full-text chest X-ray radiology reports based on a novel information extraction schema we designed to structure radiology reports. We release a development dataset, which contains board-certified radiologist annotations for 500 radiology reports from the MIMIC-CXR dataset (14,579 entities and 10,889 relations), and a test dataset, which contains two independent sets of board-certified radiologist annotations for 100 radiology reports split equally across the MIMIC-CXR and CheXpert datasets. Using these datasets, we train and test a deep learning model, RadGraph Benchmark, that achieves a micro F1 of 0.82 and 0.73 on relation extraction on the MIMIC-CXR and CheXpert test sets respectively. Additionally, we release an inference dataset, which contains annotations automatically generated by RadGraph Benchmark across 220,763 MIMIC-CXR reports (around 6 million entities and 4 million relations) and 500 CheXpert reports (13,783 entities and 9,908 relations) with mappings to associated chest radiographs. Our freely available dataset can facilitate a wide range of research in medical natural language processing, as well as computer vision and multi-modal learning when linked to chest radiographs.


Coarse-to-Fine Entity Representations for Document-level Relation Extraction

Dec 04, 2020
Damai Dai, Jing Ren, Shuang Zeng, Baobao Chang, Zhifang Sui

Document-level Relation Extraction (RE) requires extracting relations expressed within and across sentences. Recent works show that graph-based methods, usually constructing a document-level graph that captures document-aware interactions, can obtain useful entity representations thus helping tackle document-level RE. These methods either focus more on the entire graph, or pay more attention to a part of the graph, e.g., paths between the target entity pair. However, we find that document-level RE may benefit from focusing on both of them simultaneously. Therefore, to obtain more comprehensive entity representations, we propose the \textbf{C}oarse-to-\textbf{F}ine \textbf{E}ntity \textbf{R}epresentation model (\textbf{CFER}) that adopts a coarse-to-fine strategy involving two phases. First, CFER uses graph neural networks to integrate global information in the entire graph at a coarse level. Next, CFER utilizes the global information as a guidance to selectively aggregate path information between the target entity pair at a fine level. In classification, we combine the entity representations from both two levels into more comprehensive representations for relation extraction. Experimental results on a large-scale document-level RE dataset show that CFER achieves better performance than previous baseline models. Further, we verify the effectiveness of our strategy through elaborate model analysis.


ConceptBeam: Concept Driven Target Speech Extraction

Jul 25, 2022
Yasunori Ohishi, Marc Delcroix, Tsubasa Ochiai, Shoko Araki, Daiki Takeuchi, Daisuke Niizumi, Akisato Kimura, Noboru Harada, Kunio Kashino

We propose a novel framework for target speech extraction based on semantic information, called ConceptBeam. Target speech extraction means extracting the speech of a target speaker in a mixture. Typical approaches have been exploiting properties of audio signals, such as harmonic structure and direction of arrival. In contrast, ConceptBeam tackles the problem with semantic clues. Specifically, we extract the speech of speakers speaking about a concept, i.e., a topic of interest, using a concept specifier such as an image or speech. Solving this novel problem would open the door to innovative applications such as listening systems that focus on a particular topic discussed in a conversation. Unlike keywords, concepts are abstract notions, making it challenging to directly represent a target concept. In our scheme, a concept is encoded as a semantic embedding by mapping the concept specifier to a shared embedding space. This modality-independent space can be built by means of deep metric learning using paired data consisting of images and their spoken captions. We use it to bridge modality-dependent information, i.e., the speech segments in the mixture, and the specified, modality-independent concept. As a proof of our scheme, we performed experiments using a set of images associated with spoken captions. That is, we generated speech mixtures from these spoken captions and used the images or speech signals as the concept specifiers. We then extracted the target speech using the acoustic characteristics of the identified segments. We compare ConceptBeam with two methods: one based on keywords obtained from recognition systems and another based on sound source separation. We show that ConceptBeam clearly outperforms the baseline methods and effectively extracts speech based on the semantic representation.

* Accepted to ACM Multimedia 2022