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Downstream Task Performance of BERT Models Pre-Trained Using Automatically De-Identified Clinical Data
Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.ORCID iD: 0000-0001-8988-8226
Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.ORCID iD: 0000-0003-0165-9926
2022 (English)In: Proceedings of the 13th Conference on Language Resources and Evaluation (LREC 2022), European Language Resources Association , 2022, p. 4245-4252Conference paper, Published paper (Refereed)
Abstract [en]

Automatic de-identification is a cost-effective and straightforward way of removing large amounts of personally identifiable information from large and sensitive corpora. However, these systems also introduce errors into datasets due to their imperfect precision. These corruptions of the data may negatively impact the utility of the de-identified dataset. This paper de-identifies a very large clinical corpus in Swedish either by removing entire sentences containing sensitive data or by replacing sensitive words with realistic surrogates. These two datasets are used to perform domain adaptation of a general Swedish BERT model. The impact of the de-identification techniques is assessed by training and evaluating the models using six clinical downstream tasks. The results are then compared to a similar BERT model domain-adapted using an unaltered version of the clinical corpus. The results show that using an automatically de-identified corpus for domain adaptation does not negatively impact downstream performance. We argue that automatic de-identification is an efficient way of reducing the privacy risks of domain-adapted models and that the models created in this paper should be safe to distribute to other academic researchers.

Place, publisher, year, edition, pages
European Language Resources Association , 2022. p. 4245-4252
Keywords [en]
Privacy-preserving machine learning, pseudonymization, de-identification, Swedish clinical text, pre-trained language models, BERT, downstream tasks, NER, multi-label classification
National Category
Natural Language Processing
Research subject
Computer and Systems Sciences
Identifiers
URN: urn:nbn:se:su:diva-207395OAI: oai:DiVA.org:su-207395DiVA, id: diva2:1683485
Conference
Conference on Language Resources and Evaluation (LREC 2022), Marseilles, France, 21-23 June 2022
Available from: 2022-07-15 Created: 2022-07-15 Last updated: 2025-02-07
In thesis
1. Attacking and Defending the Privacy of Clinical Language Models
Open this publication in new window or tab >>Attacking and Defending the Privacy of Clinical Language Models
2023 (English)Licentiate thesis, comprehensive summary (Other academic)
Abstract [en]

The state-of-the-art methods in natural language processing (NLP) increasingly rely on large pre-trained transformer models. The strength of the models stems from their large number of parameters and the enormous amounts of data used to train them. The datasets are of a scale that makes it difficult, if not impossible, to audit them manually. When unwieldy amounts of potentially sensitive data are used to train large machine learning models, a difficult problem arises: the unintended memorization of the training data.

All datasets—including those based on publicly available data—can contain sensitive information about individuals. When models unintentionally memorize these sensitive data, they become vulnerable to different types of privacy attacks. Very few datasets for NLP can be guaranteed to be free from sensitive data. Thus, to varying degrees, most NLP models are susceptible to privacy leakage. This susceptibility is especially concerning in clinical NLP, where the data typically consist of electronic health records. Unintentionally leaking publicly available data can be problematic, but leaking data from electronic health records is never acceptable from a privacy perspective. At the same time, clinical NLP has great potential to improve the quality and efficiency of healthcare.

This licentiate thesis investigates how these privacy risks can be mitigated using automatic de-identification. This is done by exploring the privacy risks of pre-training using clinical data and then evaluating the impact on the model accuracy of decreasing these risks. A BERT model pre-trained using clinical data is subjected to a training data extraction attack. The same model is also used to evaluate a membership inference attack that has been proposed to quantify the privacy risks associated with masked language models. Then, the impact of automatic de-identification on the performance of BERT models is evaluated for both pre-training and fine-tuning data.

The results show that extracting training data from BERT models is non-trivial and suggest that the risks can be further decreased by automatically de-identifying the training data. Automatic de-identification is found to preserve the utility of the data used for pre-training and fine-tuning BERT models, resulting in no reduction in performance compared to models trained using unaltered data. However, we also find that the current state-of-the-art membership inference attacks are unable to quantify the privacy benefits of automatic de-identification. The results show that automatic de-identification reduces the privacy risks of using sensitive data for NLP without harming the utility of the data, but that these privacy benefits may be difficult to quantify.

Abstract [sv]

Den språkteknologiska forskningen blir alltmer beroende av stora förtränade transformermodeller. Dessa kraftfulla språkmodeller utgörs av ett stort antal parametrar som tränas genom att bearbeta enorma datamängder. Träningsdatan är typiskt av en sådan omfattning att det är svårt – om inte omöjligt – att granska dem manuellt. När otympliga mängder av potentiellt känsliga data används för att träna stora språkmodeller uppstår ett svårhanterligt fenomen: oavsiktlig memorering.

Väldigt få datakällor är helt fria från känsliga personuppgifter. Eftersom stora språkmodeller visat sig memorera detaljer om sina träningsdata gör det dem sårbara för integritetsröjande attacker. Denna sårbarhet är särskilt oroväckande inom klinisk språkteknologi, där data typiskt utgörs av elektroniska patientjournaler. Det är problematiskt att röja personuppgifter även om de är offentliga, men att läcka information från en individs patientjournaler är en oacceptabel integritetskränkning. Samtidigt så har klinisk språkteknologi stor potential att både förbättra kvalitén och öka effektiviteten inom sjukvården.

Denna licentiatavhandling undersöker hur de nyss nämnda integritetsriskerna kan minskas med hjälp av automatisk avidentifiering. Detta undersöks genom att först utforska riskerna med att förträna språkmodeller med kliniska träningsdata och sedan jämföra hur modellernas tillförlitlighet och prestanda påverkas av att dessa risker minskas. En BERT-modell som förtränats med kliniska data utsätts för en attack som syftar till att extrahera träningsdata. Samma modell används också för att utvärdera en föreslagen metod för att kvantifiera integritetsrisker hos maskade språkmodeller och som baseras på modellernas mottaglighet för medlemskapsinferensattacker. Därefter utvärderas hur användbara automatiskt avidentifierade data är för att förträna BERT-modeller och för att träna dem att lösa specifika språkteknologiska problem.

Resultaten visar att det är icke-trivialt att extrahera träningsdata ur språkmodeller. Samtidigt kan de risker som ändå finns minskas genom att automatiskt avidentifiera modellernas träningsdata. Därtill visar resultaten att språkmodeller tränade med automatiskt avidentifierade data fungerar lika väl som de som tränats med känsliga data. Detta gäller både vid förträning och vid träning för specifika problem. Samtidigt visar experimenten med medlemskapsinferens att nuvarande metoder inte fångar integritetsfördelarna av att automatiskt avidentifiera träningsdata. Sammanfattningsvis visar denna avhandling att automatisk avidentifiering kan användas för att minska de integritetsrisker som kommer av att använda känsliga data samtidigt som deras användbarhet bibehålls. Än saknas dock vedertagna metoder för att kvantifiera dessa integritetsvinster.

Place, publisher, year, edition, pages
Stockholm: Department of Computer and Systems Sciences, Stockholm University, 2023
Series
Report Series / Department of Computer & Systems Sciences, ISSN 1101-8526 ; 23-004
National Category
Natural Language Processing Computer Sciences
Research subject
Computer and Systems Sciences
Identifiers
urn:nbn:se:su:diva-216693 (URN)
Presentation
2023-05-15, M20, Borgarfjordsgatan 12, Kista, 10:00 (English)
Opponent
Supervisors
Available from: 2023-04-25 Created: 2023-04-24 Last updated: 2025-02-01Bibliographically approved

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Vakili, ThomasLamproudis, AnastasiosHenriksson, AronDalianis, Hercules

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