arXiv subjects

Ozlem Uzuner

Publications and source records attributed to Ozlem Uzuner.

32 records · Page 2Linked to original sources

arXiv2022

The Leaf Clinical Trials Corpus: a new resource for query generation from clinical trial eligibility criteria

Identifying cohorts of patients based on eligibility criteria such as medical conditions, procedures, and medication use is critical to recruitment for clinical trials. Such criteria are often most naturally described in free-text, using language familiar to clinicians and researchers. In order to identify potential participants at scale, these criteria must first be translated into queries on clinical databases, which can be labor-intensive and error-prone. Natural language processing (NLP) methods offer a potential means of such conversion into database queries automatically. However they must first be trained and evaluated using corpora which capture clinical trials criteria in sufficient detail. In this paper, we introduce the Leaf Clinical Trials (LCT) corpus, a human-annotated corpus of over 1,000 clinical trial eligibility criteria descriptions using highly granular structured labels capturing a range of biomedical phenomena. We provide details of our schema, annotation process, corpus quality, and statistics. Additionally, we present baseline information extraction results on this corpus as benchmarks for future work.

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arXiv2022

Online User Profiling to Detect Social Bots on Twitter

Social media platforms can expose influential trends in many aspects of everyday life. However, the movements they represent can be contaminated by disinformation. Social bots are one of the significant sources of disinformation in social media. Social bots can pose serious cyber threats to society and public opinion. This research aims to develop machine learning models to detect bots based on the extracted user's profile from a Tweet's text. Online users' profile shows the user's personal information, such as age, gender, education, and personality. In this work, the user's profile is constructed based on the user's online posts. This work's main contribution is three-fold: First, we aim to improve bot detection through machine learning models based on the user's personal information generated by the user's online comments. When comparing two online posts, the similarity of personal information makes it difficult to differentiate a bot from a human user. However, this research turns personal information similarity among two online posts into an advantage for the new bot detection model. The new proposed model for bot detection creates user profiles based on personal information such as age, personality, gender, education from users' online posts and introduces a machine learning model to detect social bots with high prediction accuracy based on personal information. Second, create a new public data set that shows the user's profile for more than 6900 Twitter accounts in the Cresci 2017 data set.

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arXiv2022

Fine-Tuning Approach for Arabic Offensive Language Detection System: BERT-Based Model

The problem of online offensive language limits the health and security of online users. It is essential to apply the latest state-of-the-art techniques in developing a system to detect online offensive language and to ensure social justice to the online communities. Our study investigates the effects of fine-tuning across several Arabic offensive language datasets. We develop multiple classifiers that use four datasets individually and in combination in order to gain knowledge about online Arabic offensive content and classify users comments accordingly. Our results demonstrate the limited effects of transfer learning on the classifiers performance, particularly for highly dialectal comments.

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arXiv2021

A Scoping Review of Publicly Available Language Tasks in Clinical Natural Language Processing

Objective: to provide a scoping review of papers on clinical natural language processing (NLP) tasks that use publicly available electronic health record data from a cohort of patients. Materials and Methods: We searched six databases, including biomedical research and computer science literature database. A round of title/abstract screening and full-text screening were conducted by two reviewers. Our method followed the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines. Results: A total of 35 papers with 47 clinical NLP tasks met inclusion criteria between 2007 and 2021. We categorized the tasks by the type of NLP problems, including name entity recognition, summarization, and other NLP tasks. Some tasks were introduced with a topic of clinical decision support applications, such as substance abuse, phenotyping, cohort selection for clinical trial. We summarized the tasks by publication and dataset information. Discussion: The breadth of clinical NLP tasks keeps growing as the field of NLP evolves with advancements in language systems. However, gaps exist in divergent interests between general domain NLP community and clinical informatics community, and in generalizability of the data sources. We also identified issues in data selection and preparation including the lack of time-sensitive data, and invalidity of problem size and evaluation. Conclusions: The existing clinical NLP tasks cover a wide range of topics and the field will continue to grow and attract more attention from both general domain NLP and clinical informatics community. We encourage future work to incorporate multi-disciplinary collaboration, reporting transparency, and standardization in data preparation.

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arXiv2021

Extracting Radiological Findings With Normalized Anatomical Information Using a Span-Based BERT Relation Extraction Model

Medical imaging is critical to the diagnosis and treatment of numerous medical problems, including many forms of cancer. Medical imaging reports distill the findings and observations of radiologists, creating an unstructured textual representation of unstructured medical images. Large-scale use of this text-encoded information requires converting the unstructured text to a structured, semantic representation. We explore the extraction and normalization of anatomical information in radiology reports that is associated with radiological findings. We investigate this extraction and normalization task using a span-based relation extraction model that jointly extracts entities and relations using BERT. This work examines the factors that influence extraction and normalization performance, including the body part/organ system, frequency of occurrence, span length, and span diversity. It discusses approaches for improving performance and creating high-quality semantic representations of radiological phenomena.

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arXiv2021

Transferability of Neural Network Clinical De-identification Systems

Objective: Neural network de-identification studies have focused on individual datasets. These studies assume the availability of a sufficient amount of human-annotated data to train models that can generalize to corresponding test data. In real-world situations, however, researchers often have limited or no in-house training data. Existing systems and external data can help jump-start de-identification on in-house data; however, the most efficient way of utilizing existing systems and external data is unclear. This article investigates the transferability of a state-of-the-art neural clinical de-identification system, NeuroNER, across a variety of datasets, when it is modified architecturally for domain generalization and when it is trained strategically for domain transfer. Methods and Materials: We conducted a comparative study of the transferability of NeuroNER using four clinical note corpora with multiple note types from two institutions. We modified NeuroNER architecturally to integrate two types of domain generalization approaches. We evaluated each architecture using three training strategies. We measured: transferability from external sources; transferability across note types; the contribution of external source data when in-domain training data are available; and transferability across institutions. Results and Conclusions: Transferability from a single external source gave inconsistent results. Using additional external sources consistently yielded an F1-score of approximately 80%. Fine-tuning emerged as a dominant transfer strategy, with or without domain generalization. We also found that external sources were useful even in cases where in-domain training data were available. Transferability across institutions differed by note type and annotation label but resulted in improved performance.

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arXiv2021

Jointly Learning Clinical Entities and Relations with Contextual Language Models and Explicit Context

We hypothesize that explicit integration of contextual information into an Multi-task Learning framework would emphasize the significance of context for boosting performance in jointly learning Named Entity Recognition (NER) and Relation Extraction (RE). Our work proves this hypothesis by segmenting entities from their surrounding context and by building contextual representations using each independent segment. This relation representation allows for a joint NER/RE system that achieves near state-of-the-art (SOTA) performance on both NER and RE tasks while beating the SOTA RE system at end-to-end NER & RE with a 49.07 F1.

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arXiv2021

Transfer Learning Approach for Arabic Offensive Language Detection System -- BERT-Based Model

Developing a system to detect online offensive language is very important to the health and the security of online users. Studies have shown that cyberhate, online harassment and other misuses of technology are on the rise, particularly during the global Coronavirus pandemic in 2020. According to the latest report by the Anti-Defamation League (ADL), 35% of online users reported online harassment related to their identity-based characteristics, which is a 3% increase over 2019. Applying advanced techniques from the Natural Language Processing (NLP) field to support the development of an online hate-free community is a critical task for social justice. Transfer learning enhances the performance of the classifier by allowing the transfer of knowledge from one domain or one dataset to others that have not been seen before, thus, supporting the classifier to be more generalizable. In our study, we apply the principles of transfer learning cross multiple Arabic offensive language datasets to compare the effects on system performance. This study aims at investigating the effects of fine-tuning and training Bidirectional Encoder Representations from Transformers (BERT) model on multiple Arabic offensive language datasets individually and testing it using other datasets individually. Our experiment starts with a comparison among multiple BERT models to guide the selection of the main model that is used for our study. The study also investigates the effects of concatenating all datasets to be used for fine-tuning and training BERT model. Our results demonstrate the limited effects of transfer learning on the performance of the classifiers, particularly for highly dialectic comments.

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arXiv2021

Exploratory Arabic Offensive Language Dataset Analysis

This paper adding more insights towards resources and datasets used in Arabic offensive language research. The main goal of this paper is to guide researchers in Arabic offensive language in selecting appropriate datasets based on their content, and in creating new Arabic offensive language resources to support and complement the available ones.

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arXiv2020

SalamNET at SemEval-2020 Task12: Deep Learning Approach for Arabic Offensive Language Detection

This paper describes SalamNET, an Arabic offensive language detection system that has been submitted to SemEval 2020 shared task 12: Multilingual Offensive Language Identification in Social Media. Our approach focuses on applying multiple deep learning models and conducting in depth error analysis of results to provide system implications for future development considerations. To pursue our goal, a Recurrent Neural Network (RNN), a Gated Recurrent Unit (GRU), and Long-Short Term Memory (LSTM) models with different design architectures have been developed and evaluated. The SalamNET, a Bi-directional Gated Recurrent Unit (Bi-GRU) based model, reports a macro-F1 score of 0.83.

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arXiv2019

Extraction and Analysis of Clinically Important Follow-up Recommendations in a Large Radiology Dataset

Communication of follow-up recommendations when abnormalities are identified on imaging studies is prone to error. In this paper, we present a natural language processing approach based on deep learning to automatically identify clinically important recommendations in radiology reports. Our approach first identifies the recommendation sentences and then extracts reason, test, and time frame of the identified recommendations. To train our extraction models, we created a corpus of 567 radiology reports annotated for recommendation information. Our extraction models achieved 0.92 f-score for recommendation sentence, 0.65 f-score for reason, 0.73 f-score for test, and 0.84 f-score for time frame. We applied the extraction models to a set of over 3.3 million radiology reports and analyzed the adherence of follow-up recommendations.

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arXiv2016

Feature-Augmented Neural Networks for Patient Note De-identification

Patient notes contain a wealth of information of potentially great interest to medical investigators. However, to protect patients' privacy, Protected Health Information (PHI) must be removed from the patient notes before they can be legally released, a process known as patient note de-identification. The main objective for a de-identification system is to have the highest possible recall. Recently, the first neural-network-based de-identification system has been proposed, yielding state-of-the-art results. Unlike other systems, it does not rely on human-engineered features, which allows it to be quickly deployed, but does not leverage knowledge from human experts or from electronic health records (EHRs). In this work, we explore a method to incorporate human-engineered features as well as features derived from EHRs to a neural-network-based de-identification system. Our results show that the addition of features, especially the EHR-derived features, further improves the state-of-the-art in patient note de-identification, including for some of the most sensitive PHI types such as patient names. Since in a real-life setting patient notes typically come with EHRs, we recommend developers of de-identification systems to leverage the information EHRs contain.

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arXiv2016

De-identification of Patient Notes with Recurrent Neural Networks

Objective: Patient notes in electronic health records (EHRs) may contain critical information for medical investigations. However, the vast majority of medical investigators can only access de-identified notes, in order to protect the confidentiality of patients. In the United States, the Health Insurance Portability and Accountability Act (HIPAA) defines 18 types of protected health information (PHI) that needs to be removed to de-identify patient notes. Manual de-identification is impractical given the size of EHR databases, the limited number of researchers with access to the non-de-identified notes, and the frequent mistakes of human annotators. A reliable automated de-identification system would consequently be of high value. Materials and Methods: We introduce the first de-identification system based on artificial neural networks (ANNs), which requires no handcrafted features or rules, unlike existing systems. We compare the performance of the system with state-of-the-art systems on two datasets: the i2b2 2014 de-identification challenge dataset, which is the largest publicly available de-identification dataset, and the MIMIC de-identification dataset, which we assembled and is twice as large as the i2b2 2014 dataset. Results: Our ANN model outperforms the state-of-the-art systems. It yields an F1-score of 97.85 on the i2b2 2014 dataset, with a recall 97.38 and a precision of 97.32, and an F1-score of 99.23 on the MIMIC de-identification dataset, with a recall 99.25 and a precision of 99.06. Conclusion: Our findings support the use of ANNs for de-identification of patient notes, as they show better performance than previously published systems while requiring no feature engineering.

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arXiv2015

Normalization of Relative and Incomplete Temporal Expressions in Clinical Narratives

We analyze the RI-TIMEXes in temporally annotated corpora and propose two hypotheses regarding the normalization of RI-TIMEXes in the clinical narrative domain: the anchor point hypothesis and the anchor relation hypothesis. We annotate the RI-TIMEXes in three corpora to study the characteristics of RI-TMEXes in different domains. This informed the design of our RI-TIMEX normalization system for the clinical domain, which consists of an anchor point classifier, an anchor relation classifier and a rule-based RI-TIMEX text span parser. We experiment with different feature sets and perform error analysis for each system component. The annotation confirmed the hypotheses that we can simplify the RI-TIMEXes normalization task using two multi-label classifiers. Our system achieves anchor point classification, anchor relation classification and rule-based parsing accuracy of 74.68%, 87.71% and 57.2% (82.09% under relaxed matching criteria) respectively on the held-out test set of the 2012 i2b2 temporal relation challenge. Experiments with feature sets reveals some interesting findings such as the verbal tense feature does not inform the anchor relation classification in clinical narratives as much as the tokens near the RI-TIMEX. Error analysis shows that underrepresented anchor point and anchor relation classes are difficult to detect. We formulate the RI-TIMEX normalization problem as a pair of multi-label classification problems. Considering only the RI-TIMEX extraction and normalization, the system achieves statistically significant improvement over the RI-TIMEX results of the best systems in the 2012 i2b2 challenge.

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