scholarly journals Deep learning models in detection of dietary supplement adverse event signals from Twitter

JAMIA Open ◽  
2021 ◽  
Vol 4 (4) ◽  
Author(s):  
Yefeng Wang ◽  
Yunpeng Zhao ◽  
Dalton Schutte ◽  
Jiang Bian ◽  
Rui Zhang
Keyword(s):  
Adverse Event ◽  
Deep Learning ◽  
Knowledge Base ◽  
Dietary Supplement ◽  
Relation Extraction ◽  
Learning Models ◽  
Concept Extraction ◽  
Annotation Guideline ◽  
End To End ◽  
Ae Signals

Abstract Objective The objective of this study is to develop a deep learning pipeline to detect signals on dietary supplement-related adverse events (DS AEs) from Twitter. Materials and Methods We obtained 247 807 tweets ranging from 2012 to 2018 that mentioned both DS and AE. We designed a tailor-made annotation guideline for DS AEs and annotated biomedical entities and relations on 2000 tweets. For the concept extraction task, we fine-tuned and compared the performance of BioClinical-BERT, PubMedBERT, ELECTRA, RoBERTa, and DeBERTa models with a CRF classifier. For the relation extraction task, we fine-tuned and compared BERT models to BioClinical-BERT, PubMedBERT, RoBERTa, and DeBERTa models. We chose the best-performing models in each task to assemble an end-to-end deep learning pipeline to detect DS AE signals and compared the results to the known DS AEs from a DS knowledge base (ie, iDISK). Results DeBERTa-CRF model outperformed other models in the concept extraction task, scoring a lenient microaveraged F1 score of 0.866. RoBERTa model outperformed other models in the relation extraction task, scoring a lenient microaveraged F1 score of 0.788. The end-to-end pipeline built on these 2 models was able to extract DS indication and DS AEs with a lenient microaveraged F1 score of 0.666. Conclusion We have developed a deep learning pipeline that can detect DS AE signals from Twitter. We have found DS AEs that were not recorded in an existing knowledge base (iDISK) and our proposed pipeline can as sist DS AE pharmacovigilance.

scholarly journals Extracting Family History of Patients From Clinical Narratives: Exploring an End-to-End Solution With Deep Learning Models (Preprint)

2020 ◽  
Author(s):  
Xi Yang ◽  
Hansi Zhang ◽  
Xing He ◽  
Jiang Bian ◽  
Yonghui Wu
Keyword(s):  
Deep Learning ◽  
Family History ◽  
Information Extraction ◽  
Language Processing ◽  
Conditional Random Fields ◽  
Short Term Memory ◽  
Majority Voting ◽  
Learning Models ◽  
Concept Extraction ◽  
End To End

BACKGROUND Patients’ family history (FH) is a critical risk factor associated with numerous diseases. However, FH information is not well captured in the structured database but often documented in clinical narratives. Natural language processing (NLP) is the key technology to extract patients’ FH from clinical narratives. In 2019, the National NLP Clinical Challenge (n2c2) organized shared tasks to solicit NLP methods for FH information extraction. OBJECTIVE This study presents our end-to-end FH extraction system developed during the 2019 n2c2 open shared task as well as the new transformer-based models that we developed after the challenge. We seek to develop a machine learning–based solution for FH information extraction without task-specific rules created by hand. METHODS We developed deep learning–based systems for FH concept extraction and relation identification. We explored deep learning models including long short-term memory-conditional random fields and bidirectional encoder representations from transformers (BERT) as well as developed ensemble models using a majority voting strategy. To further optimize performance, we systematically compared 3 different strategies to use BERT output representations for relation identification. RESULTS Our system was among the top-ranked systems (3 out of 21) in the challenge. Our best system achieved micro-averaged F1 scores of 0.7944 and 0.6544 for concept extraction and relation identification, respectively. After challenge, we further explored new transformer-based models and improved the performances of both subtasks to 0.8249 and 0.6775, respectively. For relation identification, our system achieved a performance comparable to the best system (0.6810) reported in the challenge. CONCLUSIONS This study demonstrated the feasibility of utilizing deep learning methods to extract FH information from clinical narratives.

scholarly journals Extracting Family History of Patients From Clinical Narratives: Exploring an End-to-End Solution With Deep Learning Models

10.2196/22982 ◽  
2020 ◽  
Vol 8 (12) ◽  
pp. e22982
Author(s):  
Xi Yang ◽  
Hansi Zhang ◽  
Xing He ◽  
Jiang Bian ◽  
Yonghui Wu
Keyword(s):  
Deep Learning ◽  
Family History ◽  
Information Extraction ◽  
Language Processing ◽  
Conditional Random Fields ◽  
Short Term Memory ◽  
Majority Voting ◽  
Learning Models ◽  
Concept Extraction ◽  
End To End

Background Patients’ family history (FH) is a critical risk factor associated with numerous diseases. However, FH information is not well captured in the structured database but often documented in clinical narratives. Natural language processing (NLP) is the key technology to extract patients’ FH from clinical narratives. In 2019, the National NLP Clinical Challenge (n2c2) organized shared tasks to solicit NLP methods for FH information extraction. Objective This study presents our end-to-end FH extraction system developed during the 2019 n2c2 open shared task as well as the new transformer-based models that we developed after the challenge. We seek to develop a machine learning–based solution for FH information extraction without task-specific rules created by hand. Methods We developed deep learning–based systems for FH concept extraction and relation identification. We explored deep learning models including long short-term memory-conditional random fields and bidirectional encoder representations from transformers (BERT) as well as developed ensemble models using a majority voting strategy. To further optimize performance, we systematically compared 3 different strategies to use BERT output representations for relation identification. Results Our system was among the top-ranked systems (3 out of 21) in the challenge. Our best system achieved micro-averaged F1 scores of 0.7944 and 0.6544 for concept extraction and relation identification, respectively. After challenge, we further explored new transformer-based models and improved the performances of both subtasks to 0.8249 and 0.6775, respectively. For relation identification, our system achieved a performance comparable to the best system (0.6810) reported in the challenge. Conclusions This study demonstrated the feasibility of utilizing deep learning methods to extract FH information from clinical narratives.

Deep learning for detecting logic-flaw-exploiting network attacks: An end-to-end approach

2021 ◽  
pp. 1-30
Author(s):  
Qingtian Zou ◽  
Anoop Singhal ◽  
Xiaoyan Sun ◽  
Peng Liu
Keyword(s):  
Deep Learning ◽  
Attack Detection ◽  
Network Data ◽  
Learning Models ◽  
Real World Data ◽  
Network Attacks ◽  
Network Attack ◽  
Public Network ◽  
Network Intrusion ◽  
End To End

Network attacks have become a major security concern for organizations worldwide. A category of network attacks that exploit the logic (security) flaws of a few widely-deployed authentication protocols has been commonly observed in recent years. Such logic-flaw-exploiting network attacks often do not have distinguishing signatures, and can thus easily evade the typical signature-based network intrusion detection systems. Recently, researchers have applied neural networks to detect network attacks with network logs. However, public network data sets have major drawbacks such as limited data sample variations and unbalanced data with respect to malicious and benign samples. In this paper, we present a new end-to-end approach based on protocol fuzzing to automatically generate high-quality network data, on which deep learning models can be trained for network attack detection. Our findings show that protocol fuzzing can generate data samples that cover real-world data, and deep learning models trained with fuzzed data can successfully detect the logic-flaw-exploiting network attacks.

scholarly journals A comparison of deep learning models for end-to-end face-based video retrieval in unconstrained videos

2022 ◽  
Author(s):  
Gioele Ciaparrone ◽  
Leonardo Chiariglione ◽  
Roberto Tagliaferri
Keyword(s):  
Deep Learning ◽  
Video Retrieval ◽  
Large Datasets ◽  
Validation Dataset ◽  
Learning Models ◽  
Average Precision ◽  
Query Image ◽  
Shot Detection ◽  
Independent Test ◽  
End To End

AbstractFace-based video retrieval (FBVR) is the task of retrieving videos that containing the same face shown in the query image. In this article, we present the first end-to-end FBVR pipeline that is able to operate on large datasets of unconstrained, multi-shot, multi-person videos. We adapt an existing audiovisual recognition dataset to the task of FBVR and use it to evaluate our proposed pipeline. We compare a number of deep learning models for shot detection, face detection, and face feature extraction as part of our pipeline on a validation dataset made of more than 4000 videos. We obtain 97.25% mean average precision on an independent test set, composed of more than 1000 videos. The pipeline is able to extract features from videos at $$\sim $$ ∼ 7 times the real-time speed, and it is able to perform a query on thousands of videos in less than 0.5 s.

scholarly journals Variational Deep Logic Network for Joint Inference of Entities and Relations

2021 ◽  
pp. 1-38
Author(s):  
Wenya Wang ◽  
Sinno Jialin Pan
Keyword(s):  
Deep Learning ◽  
Representation Learning ◽  
Event Extraction ◽  
Relational Reasoning ◽  
Entity Extraction ◽  
Learning Models ◽  
Joint Inference ◽  
Logic Network ◽  
End To End ◽  
Relation Prediction

Abstract Nowadays, deep learning models have been widely adopted and achieved promising results on various application domains. Despite of their intriguing performance, most deep learning models function as black-boxes, lacking explicit reasoning capabilities and explanations, which are usually essential for complex problems. Take joint inference in information extraction as an example. This task requires the identification of multiple structured knowledge from texts, which is inter-correlated, including entities, events and the relationships between them. Various deep neural networks have been proposed to jointly perform entity extraction and relation prediction, which only propagate information implicitly via representation learning. However, they fail to encode the intensive correlations between entity types and relations to enforce their co-existence. On the other hand, some approaches adopt rules to explicitly constrain certain relational facts. However, the separation of rules with representation learning usually restrains the approaches with error propagation. Moreover, the pre-defined rules are inflexible and might bring negative effects when data is noisy. To address these limitations, we propose a variational deep logic network that incorporates both representation learning and relational reasoning via the variational EM algorithm. The model consists of a deep neural network to learn high-level features with implicit interactions via the self-attention mechanism and a relational logic network to explicitly exploit target interactions. These two components are trained interactively to bring the best of both worlds. We conduct extensive experiments ranging from fine-grained sentiment terms extraction, end-to-end relation prediction to end-to-end event extraction to demonstrate the effectiveness of our proposed method.

scholarly journals An investigation of single-domain and multidomain medication and adverse drug event relation extraction from electronic health record notes using advanced deep learning models

2019 ◽  
Vol 26 (7) ◽  
pp. 646-654 ◽  
Author(s):  
Fei Li ◽  
Hong Yu
Keyword(s):  
Deep Learning ◽  
State Of The Art ◽  
Relation Extraction ◽  
Single Domain ◽  
Drug Event ◽  
Health Record ◽  
Learning Models ◽  
Domain Models ◽  
Adversarial Training ◽  
Mlp Model

Abstract Objective We aim to evaluate the effectiveness of advanced deep learning models (eg, capsule network [CapNet], adversarial training [ADV]) for single-domain and multidomain relation extraction from electronic health record (EHR) notes. Materials and Methods We built multiple deep learning models with increased complexity, namely a multilayer perceptron (MLP) model and a CapNet model for single-domain relation extraction and fully shared (FS), shared-private (SP), and adversarial training (ADV) modes for multidomain relation extraction. Our models were evaluated in 2 ways: first, we compared our models using our expert-annotated cancer (the MADE1.0 corpus) and cardio corpora; second, we compared our models with the systems in the MADE1.0 and i2b2 challenges. Results Multidomain models outperform single-domain models by 0.7%-1.4% in F1 (t test P < .05), but the results of FS, SP, and ADV modes are mixed. Our results show that the MLP model generally outperforms the CapNet model by 0.1%-1.0% in F1. In the comparisons with other systems, the CapNet model achieves the state-of-the-art result (87.2% in F1) in the cancer corpus and the MLP model generally outperforms MedEx in the cancer, cardiovascular diseases, and i2b2 corpora. Conclusions Our MLP or CapNet model generally outperforms other state-of-the-art systems in medication and adverse drug event relation extraction. Multidomain models perform better than single-domain models. However, neither the SP nor the ADV mode can always outperform the FS mode significantly. Moreover, the CapNet model is not superior to the MLP model for our corpora.

scholarly journals Training confounder-free deep learning models for medical applications

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Qingyu Zhao ◽  
Ehsan Adeli ◽  
Kilian M. Pohl
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Bone Age ◽  
Magnetic Resonance Images ◽  
Data Sets ◽  
Large Set ◽  
Learning Models ◽  
End To End ◽  
The Impact ◽  
The Relationship

AbstractThe presence of confounding effects (or biases) is one of the most critical challenges in using deep learning to advance discovery in medical imaging studies. Confounders affect the relationship between input data (e.g., brain MRIs) and output variables (e.g., diagnosis). Improper modeling of those relationships often results in spurious and biased associations. Traditional machine learning and statistical models minimize the impact of confounders by, for example, matching data sets, stratifying data, or residualizing imaging measurements. Alternative strategies are needed for state-of-the-art deep learning models that use end-to-end training to automatically extract informative features from large set of images. In this article, we introduce an end-to-end approach for deriving features invariant to confounding factors while accounting for intrinsic correlations between the confounder(s) and prediction outcome. The method does so by exploiting concepts from traditional statistical methods and recent fair machine learning schemes. We evaluate the method on predicting the diagnosis of HIV solely from Magnetic Resonance Images (MRIs), identifying morphological sex differences in adolescence from those of the National Consortium on Alcohol and Neurodevelopment in Adolescence (NCANDA), and determining the bone age from X-ray images of children. The results show that our method can accurately predict while reducing biases associated with confounders. The code is available at https://github.com/qingyuzhao/br-net.

scholarly journals Improving Cross-Domain Performance for Relation Extraction via Dependency Prediction and Information Flow Control

2019 ◽  
Author(s):  
Amir Pouran Ben Veyseh ◽  
Thien Nguyen ◽  
Dejing Dou
Keyword(s):  
Deep Learning ◽  
Information Flow ◽  
Language Processing ◽  
Relation Extraction ◽  
Learning Models ◽  
Information Flow Control ◽  
Cross Domain ◽  
Benchmark Datasets ◽  
Dependency Trees ◽  
Use Dependency

Relation Extraction (RE) is one of the fundamental tasks in Information Extraction and Natural Language Processing. Dependency trees have been shown to be a very useful source of information for this task. The current deep learning models for relation extraction has mainly exploited this dependency information by guiding their computation along the structures of the dependency trees. One potential problem with this approach is it might prevent the models from capturing important context information beyond syntactic structures and cause the poor cross-domain generalization. This paper introduces a novel method to use dependency trees in RE for deep learning models that jointly predicts dependency and semantics relations. We also propose a new mechanism to control the information flow in the model based on the input entity mentions. Our extensive experiments on benchmark datasets show that the proposed model outperforms the existing methods for RE significantly.

scholarly journals SEVEN: Deep Semi-supervised Verification Networks

2017 ◽  
Author(s):  
Vahid Noroozi ◽  
Lei Zheng ◽  
Sara Bahaadini ◽  
Sihong Xie ◽  
Philip S. Yu
Keyword(s):  
Deep Learning ◽  
State Of The Art ◽  
Learning Models ◽  
Fingerprint Verification ◽  
Short Supply ◽  
Two Samples ◽  
End To End

Verification determines whether two samples belong to the same class or not, and has important applications such as face and fingerprint verification, where thousands or millions of categories are present but each category has scarce labeled examples, presenting two major challenges for existing deep learning models. We propose a deep semi-supervised model named SEmi-supervised VErification Network (SEVEN) to address these challenges. The model consists of two complementary components. The generative component addresses the lack of supervision within each category by learning general salient structures from a large amount of data across categories. The discriminative component exploits the learned general features to mitigate the lack of supervision within categories, and also directs the generative component to find more informative structures of the whole data manifold. The two components are tied together in SEVEN to allow an end-to-end training of the two components. Extensive experiments on four verification tasks demonstrate that SEVEN significantly outperforms other state-of-the-art deep semi-supervised techniques when labeled data are in short supply. Furthermore, SEVEN is competitive with fully supervised baselines trained with a larger amount of labeled data. It indicates the importance of the generative component in SEVEN.

Sign in / Sign up

Export Citation Format

Share Document