Many models are pretrained on redacted text for privacy reasons. Clinical foundation models are often trained on de-identified text, which uses special syntax (masked) text in place of protected health information. Even though these models have increased in popularity, there has been little effort in understanding the effects of training them on redacted text. In this work, we pretrain several encoder-only models on a dataset that contains redacted text and a version with replaced realistic pseudo text. We then fine-tuned models for the protected health information de-identification task and show how our methods significantly outperform previous baselines. The contributions of this work include: a) our novel, and yet surprising findings with training recommendations, b) redacted text replacements used to produce the pseudo dataset, c) pretrained embeddings and fine-tuned task specific models, and d) freely available pseudo training dataset generation and model source code used in our experiments.
Clinical data is fundamental to advance neurosurgical research, but access is often constrained by data availability, small sample sizes, privacy regulations, and resource-intensive preprocessing and de-identification procedures. Synthetic data offers a potential solution to challenges associated with accessing and using real-world data (RWD). This study aims to evaluate the capability of zero-shot generation of synthetic neurosurgical data with a large language model (LLM), GPT-4o, by benchmarking with the conditional tabular generative adversarial network (CTGAN). Synthetic datasets were compared to real-world neurosurgical data to assess fidelity (means, proportions, distributions, and bivariate correlations), utility (ML classifier performance on RWD), and privacy (duplication of records from RWD). The GPT-4o-generated datasets matched or exceeded CTGAN performance, despite no fine-tuning or access to RWD for pre-training. Datasets demonstrated high univariate and bivariate fidelity to RWD without directly exposing any real patient records, even at amplified sample size. Training an ML classifier on GPT-4o-generated data and testing on RWD for a binary prediction task showed an F1 score (0.706) with comparable performance to training on the CTGAN data (0.705) for predicting postoperative functional status deterioration. GPT-4o demonstrated a promising ability to generate high-fidelity synthetic neurosurgical data. These findings also indicate that data synthesized with GPT-4o can effectively augment clinical data with small sample sizes, and train ML models for prediction of neurosurgical outcomes. Further investigation is necessary to improve the preservation of distributional characteristics and boost classifier performance.
Generative models, particularly text-to-image (T2I) diffusion models, play a crucial role in medical image analysis. However, these models are prone to training data memorization, posing significant risks to patient privacy. Synthetic chest X-ray generation is one of the most common applications in medical image analysis with the MIMIC-CXR dataset serving as the primary data repository for this task. This study presents the first systematic attempt to identify prompts and text tokens in MIMIC-CXR that contribute the most to training data memorization. Our analysis reveals two unexpected findings: (1) prompts containing traces of de-identification procedures (markers introduced to hide Protected Health Information) are the most memorized, and (2) among all tokens, de-identification markers contribute the most towards memorization. This highlights a broader issue with the standard anonymization practices and T2I synthesis with MIMIC-CXR. To exacerbate, existing inference-time memorization mitigation strategies are ineffective and fail to sufficiently reduce the model's reliance on memorized text tokens. On this front, we propose actionable strategies for different stakeholders to enhance privacy and improve the reliability of generative models in medical imaging. Finally, our results provide a foundation for future work on developing and benchmarking memorization mitigation techniques for synthetic chest X-ray generation using the MIMIC-CXR dataset. The anonymized code is available at https://anonymous.4open.science/r/diffusion_memorization-8011/
Protecting Personally Identifiable Information (PII), such as names, is a critical requirement in learning technologies to safeguard student and teacher privacy and maintain trust. Accurate PII detection is an essential step toward anonymizing sensitive information while preserving the utility of educational data. Motivated by recent advancements in artificial intelligence, our study investigates the GPT-4o-mini model as a cost-effective and efficient solution for PII detection tasks. We explore both prompting and fine-tuning approaches and compare GPT-4o-mini's performance against established frameworks, including Microsoft Presidio and Azure AI Language. Our evaluation on two public datasets, CRAPII and TSCC, demonstrates that the fine-tuned GPT-4o-mini model achieves superior performance, with a recall of 0.9589 on CRAPII. Additionally, fine-tuned GPT-4o-mini significantly improves precision scores (a threefold increase) while reducing computational costs to nearly one-tenth of those associated with Azure AI Language. Furthermore, our bias analysis reveals that the fine-tuned GPT-4o-mini model consistently delivers accurate results across diverse cultural backgrounds and genders. The generalizability analysis using the TSCC dataset further highlights its robustness, achieving a recall of 0.9895 with minimal additional training data from TSCC. These results emphasize the potential of fine-tuned GPT-4o-mini as an accurate and cost-effective tool for PII detection in educational data. It offers robust privacy protection while preserving the data's utility for research and pedagogical analysis. Our code is available on GitHub: https://github.com/AnonJD/PrivacyAI
In recent years, there has been an increasing interest in image anonymization, particularly focusing on the de-identification of faces and individuals. However, for self-driving applications, merely de-identifying faces and individuals might not provide sufficient privacy protection since street views like vehicles and buildings can still disclose locations, trajectories, and other sensitive information. Therefore, it remains crucial to extend anonymization techniques to street view images to fully preserve the privacy of users, pedestrians, and vehicles. In this paper, we propose a Street View Image Anonymization (SVIA) framework for self-driving applications. The SVIA framework consists of three integral components: a semantic segmenter to segment an input image into functional regions, an inpainter to generate alternatives to privacy-sensitive regions, and a harmonizer to seamlessly stitch modified regions to guarantee visual coherence. Compared to existing methods, SVIA achieves a much better trade-off between image generation quality and privacy protection, as evidenced by experimental results for five common metrics on two widely used public datasets.
Face de-identification (DeID) has been widely studied for common scenes, but remains under-researched for medical scenes, mostly due to the lack of large-scale patient face datasets. In this paper, we release MeMa, consisting of over 40,000 photo-realistic patient faces. MeMa is re-generated from massive real patient photos. By carefully modulating the generation and data-filtering procedures, MeMa avoids breaching real patient privacy, while ensuring rich and plausible medical manifestations. We recruit expert clinicians to annotate MeMa with both coarse- and fine-grained labels, building the first medical-scene DeID benchmark. Additionally, we propose a baseline approach for this new medical-aware DeID task, by integrating data-driven medical semantic priors into the DeID procedure. Despite its conciseness and simplicity, our approach substantially outperforms previous ones. Dataset is available at https://github.com/tianyuan168326/MeMa-Pytorch.
Since the COVID-19 pandemic, clinicians have seen a large and sustained influx in patient portal messages, significantly contributing to clinician burnout. To the best of our knowledge, there are no large-scale public patient portal messages corpora researchers can use to build tools to optimize clinician portal workflows. Informed by our ongoing work with a regional hospital, this study introduces an LLM-powered framework for configurable and realistic patient portal message generation. Our approach leverages few-shot grounded text generation, requiring only a small number of de-identified patient portal messages to help LLMs better match the true style and tone of real data. Clinical experts in our team deem this framework as HIPAA-friendly, unlike existing privacy-preserving approaches to synthetic text generation which cannot guarantee all sensitive attributes will be protected. Through extensive quantitative and human evaluation, we show that our framework produces data of higher quality than comparable generation methods as well as all related datasets. We believe this work provides a path forward for (i) the release of large-scale synthetic patient message datasets that are stylistically similar to ground-truth samples and (ii) HIPAA-friendly data generation which requires minimal human de-identification efforts.
Recent advancements in artificial intelligence promise ample potential in monitoring applications with surveillance cameras. However, concerns about privacy and model bias have made it challenging to utilize them in public. Although de-identification approaches have been proposed in the literature, aiming to achieve a certain level of anonymization, most of them employ deep learning models that are computationally demanding for real-time edge deployment. In this study, we revisit conventional anonymization solutions for privacy protection and real-time video anomaly detection (VAD) applications. We propose a novel lightweight adaptive anonymization for VAD (LA3D) that employs dynamic adjustment to enhance privacy protection. We evaluated the approaches on publicly available privacy and VAD data sets to examine the strengths and weaknesses of the different anonymization techniques and highlight the promising efficacy of our approach. Our experiment demonstrates that LA3D enables substantial improvement in the privacy anonymization capability without majorly degrading VAD efficacy.
Medical data employed in research frequently comprises sensitive patient health information (PHI), which is subject to rigorous legal frameworks such as the General Data Protection Regulation (GDPR) or the Health Insurance Portability and Accountability Act (HIPAA). Consequently, these types of data must be pseudonymized prior to utilisation, which presents a significant challenge for many researchers. Given the vast array of medical data, it is necessary to employ a variety of de-identification techniques. To facilitate the anonymization process for medical imaging data, we have developed an open-source tool that can be used to de-identify DICOM magnetic resonance images, computer tomography images, whole slide images and magnetic resonance twix raw data. Furthermore, the implementation of a neural network enables the removal of text within the images. The proposed tool automates an elaborate anonymization pipeline for multiple types of inputs, reducing the need for additional tools used for de-identification of imaging data. We make our code publicly available at https://github.com/code-lukas/medical_image_deidentification.
De-identification is important in protecting patients' privacy for healthcare text analytics. The MASK framework is one of the best on the de-identification shared task organised by n2c2/i2b2 challenges. This work enhances the MASK framework by integrating ClinicalBERT, a deep learning model specifically fine-tuned on clinical texts, alongside traditional de-identification methods like dictionary lookup and rule-based approaches. The system effectively identifies and either redacts or replaces sensitive identifiable entities within clinical documents, while also allowing users to customise the masked documents according to their specific needs. The integration of ClinicalBERT significantly improves the performance of entity recognition, achieving 0.9732 F1-score, especially for common entities such as names, dates, and locations. A risk assessment feature has also been developed, which analyses the uniqueness of context within documents to classify them into risk levels, guiding further de-identification efforts. While the system demonstrates strong overall performance, this work highlights areas for future improvement, including handling more complex entity occurrences and enhancing the system's adaptability to different clinical settings.
The vast amount of available medical records has the potential to improve healthcare and biomedical research. However, privacy restrictions make these data accessible for internal use only. Recent works have addressed this problem by generating synthetic data using Causal Language Modeling. Unfortunately, by taking this approach, it is often impossible to guarantee patient privacy while offering the ability to control the diversity of generations without increasing the cost of generating such data. In contrast, we present a system for generating synthetic free-text medical records using Masked Language Modeling. The system preserves critical medical information while introducing diversity in the generations and minimising re-identification risk. The system's size is about 120M parameters, minimising inference cost. The results demonstrate high-quality synthetic data with a HIPAA-compliant PHI recall rate of 96% and a re-identification risk of 3.5%. Moreover, downstream evaluations show that the generated data can effectively train a model with performance comparable to real data.
The consequences of a healthcare data breach can be devastating for the patients, providers, and payers. The average financial impact of a data breach in recent months has been estimated to be close to USD 10 million. This is especially significant for healthcare organizations in India that are managing rapid digitization while still establishing data governance procedures that align with the letter and spirit of the law. Computer-based systems for de-identification of personal information are vulnerable to data drift, often rendering them ineffective in cross-institution settings. Therefore, a rigorous assessment of existing de-identification against local health datasets is imperative to support the safe adoption of digital health initiatives in India. Using a small set of de-identified patient discharge summaries provided by an Indian healthcare institution, in this paper, we report the nominal performance of de-identification algorithms (based on language models) trained on publicly available non-Indian datasets, pointing towards a lack of cross-institutional generalization. Similarly, experimentation with off-the-shelf de-identification systems reveals potential risks associated with the approach. To overcome data scarcity, we explore generating synthetic clinical reports (using publicly available and Indian summaries) by performing in-context learning over Large Language Models (LLMs). Our experiments demonstrate the use of generated reports as an effective strategy for creating high-performing de-identification systems with good generalization capabilities.
Sharing private data for learning tasks is pivotal for transparent and secure machine learning applications. Many privacy-preserving techniques have been proposed for this task aiming to transform the data while ensuring the privacy of individuals. Some of these techniques have been incorporated into tools, whereas others are accessed through various online platforms. However, such tools require manual configuration, which can be complex and time-consuming. Moreover, they require substantial expertise, potentially restricting their use to those with advanced technical knowledge. In this paper, we propose AUTOPRIV, the first automated privacy-preservation method, that eliminates the need for any manual configuration. AUTOPRIV employs meta-learning to automate the de-identification process, facilitating the secure release of data for machine learning tasks. The main goal is to anticipate the predictive performance and privacy risk of a large set of privacy configurations. We provide a ranked list of the most promising solutions, which are likely to achieve an optimal approximation within a new domain. AUTOPRIV is highly effective as it reduces computational complexity and energy consumption considerably.
To make medical datasets accessible without sharing sensitive patient information, we introduce a novel end-to-end approach for generative de-identification of dynamic medical imaging data. Until now, generative methods have faced constraints in terms of fidelity, spatio-temporal coherence, and the length of generation, failing to capture the complete details of dataset distributions. We present a model designed to produce high-fidelity, long and complete data samples with near-real-time efficiency and explore our approach on a challenging task: generating echocardiogram videos. We develop our generation method based on diffusion models and introduce a protocol for medical video dataset anonymization. As an exemplar, we present EchoNet-Synthetic, a fully synthetic, privacy-compliant echocardiogram dataset with paired ejection fraction labels. As part of our de-identification protocol, we evaluate the quality of the generated dataset and propose to use clinical downstream tasks as a measurement on top of widely used but potentially biased image quality metrics. Experimental outcomes demonstrate that EchoNet-Synthetic achieves comparable dataset fidelity to the actual dataset, effectively supporting the ejection fraction regression task. Code, weights and dataset are available at https://github.com/HReynaud/EchoNet-Synthetic.
Since the release of the original CheXpert paper five years ago, CheXpert has become one of the most widely used and cited clinical AI datasets. The emergence of vision language models has sparked an increase in demands for sharing reports linked to CheXpert images, along with a growing interest among AI fairness researchers in obtaining demographic data. To address this, CheXpert Plus serves as a new collection of radiology data sources, made publicly available to enhance the scaling, performance, robustness, and fairness of models for all subsequent machine learning tasks in the field of radiology. CheXpert Plus is the largest text dataset publicly released in radiology, with a total of 36 million text tokens, including 13 million impression tokens. To the best of our knowledge, it represents the largest text de-identification effort in radiology, with almost 1 million PHI spans anonymized. It is only the second time that a large-scale English paired dataset has been released in radiology, thereby enabling, for the first time, cross-institution training at scale. All reports are paired with high-quality images in DICOM format, along with numerous image and patient metadata covering various clinical and socio-economic groups, as well as many pathology labels and RadGraph annotations. We hope this dataset will boost research for AI models that can further assist radiologists and help improve medical care. Data is available at the following URL: https://stanfordaimi.azurewebsites.net/datasets/5158c524-d3ab-4e02-96e9-6ee9efc110a1 Models are available at the following URL: https://github.com/Stanford-AIMI/chexpert-plus
[Abridged Abstract] Recent technological advances underscore labor market dynamics, yielding significant consequences for employment prospects and increasing job vacancy data across platforms and languages. Aggregating such data holds potential for valuable insights into labor market demands, new skills emergence, and facilitating job matching for various stakeholders. However, despite prevalent insights in the private sector, transparent language technology systems and data for this domain are lacking. This thesis investigates Natural Language Processing (NLP) technology for extracting relevant information from job descriptions, identifying challenges including scarcity of training data, lack of standardized annotation guidelines, and shortage of effective extraction methods from job ads. We frame the problem, obtaining annotated data, and introducing extraction methodologies. Our contributions include job description datasets, a de-identification dataset, and a novel active learning algorithm for efficient model training. We propose skill extraction using weak supervision, a taxonomy-aware pre-training methodology adapting multilingual language models to the job market domain, and a retrieval-augmented model leveraging multiple skill extraction datasets to enhance overall performance. Finally, we ground extracted information within a designated taxonomy.
Face de-identification in videos is a challenging task in the domain of computer vision, primarily used in privacy-preserving applications. Despite the considerable progress achieved through generative vision models, there remain multiple challenges in the latest approaches. They lack a comprehensive discussion and evaluation of aspects such as realism, temporal coherence, and preservation of non-identifiable features. In our work, we propose RID-Twin: a novel pipeline that leverages the state-of-the-art generative models, and decouples identity from motion to perform automatic face de-identification in videos. We investigate the task from a holistic point of view and discuss how our approach addresses the pertinent existing challenges in this domain. We evaluate the performance of our methodology on the widely employed VoxCeleb2 dataset, and also a custom dataset designed to accommodate the limitations of certain behavioral variations absent in the VoxCeleb2 dataset. We discuss the implications and advantages of our work and suggest directions for future research.
Electronic Health Records (EHRs) are rich sources of patient-level data, offering valuable resources for medical data analysis. However, privacy concerns often restrict access to EHRs, hindering downstream analysis. Current EHR de-identification methods are flawed and can lead to potential privacy leakage. Additionally, existing publicly available EHR databases are limited, preventing the advancement of medical research using EHR. This study aims to overcome these challenges by generating realistic and privacy-preserving synthetic electronic health records (EHRs) time series efficiently. We introduce a new method for generating diverse and realistic synthetic EHR time series data using Denoising Diffusion Probabilistic Models (DDPM). We conducted experiments on six databases: Medical Information Mart for Intensive Care III and IV (MIMIC-III/IV), the eICU Collaborative Research Database (eICU), and non-EHR datasets on Stocks and Energy. We compared our proposed method with eight existing methods. Our results demonstrate that our approach significantly outperforms all existing methods in terms of data fidelity while requiring less training effort. Additionally, data generated by our method yields a lower discriminative accuracy compared to other baseline methods, indicating the proposed method can generate data with less privacy risk. The proposed diffusion-model-based method can reliably and efficiently generate synthetic EHR time series, which facilitates the downstream medical data analysis. Our numerical results show the superiority of the proposed method over all other existing methods.
With the rise of open data, identifiability of individuals based on 3D renderings obtained from routine structural magnetic resonance imaging (MRI) scans of the head has become a growing privacy concern. To protect subject privacy, several algorithms have been developed to de-identify imaging data using blurring, defacing or refacing. Completely removing facial structures provides the best re-identification protection but can significantly impact post-processing steps, like brain morphometry. As an alternative, refacing methods that replace individual facial structures with generic templates have a lower effect on the geometry and intensity distribution of original scans, and are able to provide more consistent post-processing results by the price of higher re-identification risk and computational complexity. In the current study, we propose a novel method for anonymised face generation for defaced 3D T1-weighted scans based on a 3D conditional generative adversarial network. To evaluate the performance of the proposed de-identification tool, a comparative study was conducted between several existing defacing and refacing tools, with two different segmentation algorithms (FAST and Morphobox). The aim was to evaluate (i) impact on brain morphometry reproducibility, (ii) re-identification risk, (iii) balance between (i) and (ii), and (iv) the processing time. The proposed method takes 9 seconds for face generation and is suitable for recovering consistent post-processing results after defacing.
The increasing number of benchmarks for Natural Language Processing (NLP) tasks in the computational job market domain highlights the demand for methods that can handle job-related tasks such as skill extraction, skill classification, job title classification, and de-identification. While some approaches have been developed that are specific to the job market domain, there is a lack of generalized, multilingual models and benchmarks for these tasks. In this study, we introduce a language model called ESCOXLM-R, based on XLM-R, which uses domain-adaptive pre-training on the European Skills, Competences, Qualifications and Occupations (ESCO) taxonomy, covering 27 languages. The pre-training objectives for ESCOXLM-R include dynamic masked language modeling and a novel additional objective for inducing multilingual taxonomical ESCO relations. We comprehensively evaluate the performance of ESCOXLM-R on 6 sequence labeling and 3 classification tasks in 4 languages and find that it achieves state-of-the-art results on 6 out of 9 datasets. Our analysis reveals that ESCOXLM-R performs better on short spans and outperforms XLM-R on entity-level and surface-level span-F1, likely due to ESCO containing short skill and occupation titles, and encoding information on the entity-level.