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Apr 2

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.

  • 4 authors
·
Jun 10, 2016

Improving the Performance of Radiology Report De-identification with Large-Scale Training and Benchmarking Against Cloud Vendor Methods

Objective: To enhance automated de-identification of radiology reports by scaling transformer-based models through extensive training datasets and benchmarking performance against commercial cloud vendor systems for protected health information (PHI) detection. Materials and Methods: In this retrospective study, we built upon a state-of-the-art, transformer-based, PHI de-identification pipeline by fine-tuning on two large annotated radiology corpora from Stanford University, encompassing chest X-ray, chest CT, abdomen/pelvis CT, and brain MR reports and introducing an additional PHI category (AGE) into the architecture. Model performance was evaluated on test sets from Stanford and the University of Pennsylvania (Penn) for token-level PHI detection. We further assessed (1) the stability of synthetic PHI generation using a "hide-in-plain-sight" method and (2) performance against commercial systems. Precision, recall, and F1 scores were computed across all PHI categories. Results: Our model achieved overall F1 scores of 0.973 on the Penn dataset and 0.996 on the Stanford dataset, outperforming or maintaining the previous state-of-the-art model performance. Synthetic PHI evaluation showed consistent detectability (overall F1: 0.959 [0.958-0.960]) across 50 independently de-identified Penn datasets. Our model outperformed all vendor systems on synthetic Penn reports (overall F1: 0.960 vs. 0.632-0.754). Discussion: Large-scale, multimodal training improved cross-institutional generalization and robustness. Synthetic PHI generation preserved data utility while ensuring privacy. Conclusion: A transformer-based de-identification model trained on diverse radiology datasets outperforms prior academic and commercial systems in PHI detection and establishes a new benchmark for secure clinical text processing.

  • 8 authors
·
Nov 6, 2025

RISE Controller Tuning and System Identification Through Machine Learning for Human Lower Limb Rehabilitation via Neuromuscular Electrical Stimulation

Neuromuscular electrical stimulation (NMES) has been effectively applied in many rehabilitation treatments of individuals with spinal cord injury (SCI). In this context, we introduce a novel, robust, and intelligent control-based methodology to closed-loop NMES systems. Our approach utilizes a robust control law to guarantee system stability and machine learning tools to optimize both the controller parameters and system identification. Regarding the latter, we introduce the use of past rehabilitation data to build more realistic data-driven identified models. Furthermore, we apply the proposed methodology for the rehabilitation of lower limbs using a control technique named the robust integral of the sign of the error (RISE), an offline improved genetic algorithm optimizer, and neural network models. Although in the literature, the RISE controller presented good results on healthy subjects, without any fine-tuning method, a trial and error approach would quickly lead to muscle fatigue for individuals with SCI. In this paper, for the first time, the RISE controller is evaluated with two paraplegic subjects in one stimulation session and with seven healthy individuals in at least two and at most five sessions. The results showed that the proposed approach provided a better control performance than empirical tuning, which can avoid premature fatigue on NMES-based clinical procedures.

  • 7 authors
·
Jun 28, 2020

Brazilian Portuguese Image Captioning with Transformers: A Study on Cross-Native-Translated Dataset

Image captioning (IC) refers to the automatic generation of natural language descriptions for images, with applications ranging from social media content generation to assisting individuals with visual impairments. While most research has been focused on English-based models, low-resource languages such as Brazilian Portuguese face significant challenges due to the lack of specialized datasets and models. Several studies create datasets by automatically translating existing ones to mitigate resource scarcity. This work addresses this gap by proposing a cross-native-translated evaluation of Transformer-based vision and language models for Brazilian Portuguese IC. We use a version of Flickr30K comprised of captions manually created by native Brazilian Portuguese speakers and compare it to a version with captions automatically translated from English to Portuguese. The experiments include a cross-context approach, where models trained on one dataset are tested on the other to assess the translation impact. Additionally, we incorporate attention maps for model inference interpretation and use the CLIP-Score metric to evaluate the image-description alignment. Our findings show that Swin-DistilBERTimbau consistently outperforms other models, demonstrating strong generalization across datasets. ViTucano, a Brazilian Portuguese pre-trained VLM, surpasses larger multilingual models (GPT-4o, LLaMa 3.2 Vision) in traditional text-based evaluation metrics, while GPT-4 models achieve the highest CLIP-Score, highlighting improved image-text alignment. Attention analysis reveals systematic biases, including gender misclassification, object enumeration errors, and spatial inconsistencies. The datasets and the models generated and analyzed during the current study are available in: https://github.com/laicsiifes/transformer-caption-ptbr.

  • 4 authors
·
Jan 30

GorillaWatch: An Automated System for In-the-Wild Gorilla Re-Identification and Population Monitoring

Monitoring critically endangered western lowland gorillas is currently hampered by the immense manual effort required to re-identify individuals from vast archives of camera trap footage. The primary obstacle to automating this process has been the lack of large-scale, "in-the-wild" video datasets suitable for training robust deep learning models. To address this gap, we introduce a comprehensive benchmark with three novel datasets: Gorilla-SPAC-Wild, the largest video dataset for wild primate re-identification to date; Gorilla-Berlin-Zoo, for assessing cross-domain re-identification generalization; and Gorilla-SPAC-MoT, for evaluating multi-object tracking in camera trap footage. Building on these datasets, we present GorillaWatch, an end-to-end pipeline integrating detection, tracking, and re-identification. To exploit temporal information, we introduce a multi-frame self-supervised pretraining strategy that leverages consistency in tracklets to learn domain-specific features without manual labels. To ensure scientific validity, a differentiable adaptation of AttnLRP verifies that our model relies on discriminative biometric traits rather than background correlations. Extensive benchmarking subsequently demonstrates that aggregating features from large-scale image backbones outperforms specialized video architectures. Finally, we address unsupervised population counting by integrating spatiotemporal constraints into standard clustering to mitigate over-segmentation. We publicly release all code and datasets to facilitate scalable, non-invasive monitoring of endangered species

  • 14 authors
·
Dec 8, 2025

Étude cognitive des processus de construction d'une requête dans un système de gestion de connaissances médicales

This article presents the Cogni-CISMeF project, which aims at improving medical information search in the CISMeF system (Catalog and Index of French-language health resources) by including a conversational agent to interact with the user in natural language. To study the cognitive processes involved during the information search, a bottom-up methodology was adopted. Experimentation has been set up to obtain human dialogs between a user (playing the role of patient) dealing with medical information search and a CISMeF expert refining the request. The analysis of these dialogs underlined the use of discursive evidence: vocabulary, reformulation, implicit or explicit expression of user intentions, conversational sequences, etc. A model of artificial agent is proposed. It leads the user in its information search by proposing to him examples, assistance and choices. This model was implemented and integrated in the CISMeF system. ---- Cet article d\'ecrit le projet Cogni-CISMeF qui propose un module de dialogue Homme-Machine \`a int\'egrer dans le syst\`eme d'indexation de connaissances m\'edicales CISMeF (Catalogue et Index des Sites M\'edicaux Francophones). Nous avons adopt\'e une d\'emarche de mod\'elisation cognitive en proc\'edant \`a un recueil de corpus de dialogues entre un utilisateur (jouant le r\^ole d'un patient) d\'esirant une information m\'edicale et un expert CISMeF af inant cette demande pour construire la requ\^ete. Nous avons analys\'e la structure des dialogues ainsi obtenus et avons \'etudi\'e un certain nombre d'indices discursifs : vocabulaire employ\'e, marques de reformulation, commentaires m\'eta et \'epilinguistiques, expression implicite ou explicite des intentions de l'utilisateur, encha\^inement conversationnel, etc. De cette analyse, nous avons construit un mod\`ele d'agent artificiel dot\'e de capacit\'es cognitives capables d'aider l'utilisateur dans sa t\^ache de recherche d'information. Ce mod\`ele a \'et\'e impl\'ement\'e et int\'egr\'e dans le syst\`eme CISMeF.

  • 5 authors
·
Feb 10, 2014

Keypoint Promptable Re-Identification

Occluded Person Re-Identification (ReID) is a metric learning task that involves matching occluded individuals based on their appearance. While many studies have tackled occlusions caused by objects, multi-person occlusions remain less explored. In this work, we identify and address a critical challenge overlooked by previous occluded ReID methods: the Multi-Person Ambiguity (MPA) arising when multiple individuals are visible in the same bounding box, making it impossible to determine the intended ReID target among the candidates. Inspired by recent work on prompting in vision, we introduce Keypoint Promptable ReID (KPR), a novel formulation of the ReID problem that explicitly complements the input bounding box with a set of semantic keypoints indicating the intended target. Since promptable re-identification is an unexplored paradigm, existing ReID datasets lack the pixel-level annotations necessary for prompting. To bridge this gap and foster further research on this topic, we introduce Occluded-PoseTrack ReID, a novel ReID dataset with keypoints labels, that features strong inter-person occlusions. Furthermore, we release custom keypoint labels for four popular ReID benchmarks. Experiments on person retrieval, but also on pose tracking, demonstrate that our method systematically surpasses previous state-of-the-art approaches on various occluded scenarios. Our code, dataset and annotations are available at https://github.com/VlSomers/keypoint_promptable_reidentification.

  • 3 authors
·
Jul 25, 2024

Character Detection using YOLO for Writer Identification in multiple Medieval books

Paleography is the study of ancient and historical handwriting, its key objectives include the dating of manuscripts and understanding the evolution of writing. Estimating when a document was written and tracing the development of scripts and writing styles can be aided by identifying the individual scribes who contributed to a medieval manuscript. Although digital technologies have made significant progress in this field, the general problem remains unsolved and continues to pose open challenges. ... We previously proposed an approach focused on identifying specific letters or abbreviations that characterize each writer. In that study, we considered the letter "a", as it was widely present on all pages of text and highly distinctive, according to the suggestions of expert paleographers. We used template matching techniques to detect the occurrences of the character "a" on each page and the convolutional neural network (CNN) to attribute each instance to the correct scribe. Moving from the interesting results achieved from this previous system and being aware of the limitations of the template matching technique, which requires an appropriate threshold to work, we decided to experiment in the same framework with the use of the YOLO object detection model to identify the scribe who contributed to the writing of different medieval books. We considered the fifth version of YOLO to implement the YOLO object detection model, which completely substituted the template matching and CNN used in the previous work. The experimental results demonstrate that YOLO effectively extracts a greater number of letters considered, leading to a more accurate second-stage classification. Furthermore, the YOLO confidence score provides a foundation for developing a system that applies a rejection threshold, enabling reliable writer identification even in unseen manuscripts.

  • 5 authors
·
Jan 8

DeID-GPT: Zero-shot Medical Text De-Identification by GPT-4

The digitization of healthcare has facilitated the sharing and re-using of medical data but has also raised concerns about confidentiality and privacy. HIPAA (Health Insurance Portability and Accountability Act) mandates removing re-identifying information before the dissemination of medical records. Thus, effective and efficient solutions for de-identifying medical data, especially those in free-text forms, are highly needed. While various computer-assisted de-identification methods, including both rule-based and learning-based, have been developed and used in prior practice, such solutions still lack generalizability or need to be fine-tuned according to different scenarios, significantly imposing restrictions in wider use. The advancement of large language models (LLM), such as ChatGPT and GPT-4, have shown great potential in processing text data in the medical domain with zero-shot in-context learning, especially in the task of privacy protection, as these models can identify confidential information by their powerful named entity recognition (NER) capability. In this work, we developed a novel GPT4-enabled de-identification framework (``DeID-GPT") to automatically identify and remove the identifying information. Compared to existing commonly used medical text data de-identification methods, our developed DeID-GPT showed the highest accuracy and remarkable reliability in masking private information from the unstructured medical text while preserving the original structure and meaning of the text. This study is one of the earliest to utilize ChatGPT and GPT-4 for medical text data processing and de-identification, which provides insights for further research and solution development on the use of LLMs such as ChatGPT/GPT-4 in healthcare. Codes and benchmarking data information are available at https://github.com/yhydhx/ChatGPT-API.

  • 18 authors
·
Mar 20, 2023

Large-scale Training Data Search for Object Re-identification

We consider a scenario where we have access to the target domain, but cannot afford on-the-fly training data annotation, and instead would like to construct an alternative training set from a large-scale data pool such that a competitive model can be obtained. We propose a search and pruning (SnP) solution to this training data search problem, tailored to object re-identification (re-ID), an application aiming to match the same object captured by different cameras. Specifically, the search stage identifies and merges clusters of source identities which exhibit similar distributions with the target domain. The second stage, subject to a budget, then selects identities and their images from the Stage I output, to control the size of the resulting training set for efficient training. The two steps provide us with training sets 80\% smaller than the source pool while achieving a similar or even higher re-ID accuracy. These training sets are also shown to be superior to a few existing search methods such as random sampling and greedy sampling under the same budget on training data size. If we release the budget, training sets resulting from the first stage alone allow even higher re-ID accuracy. We provide interesting discussions on the specificity of our method to the re-ID problem and particularly its role in bridging the re-ID domain gap. The code is available at https://github.com/yorkeyao/SnP.

  • 4 authors
·
Mar 28, 2023

LLMs-in-the-Loop Part 2: Expert Small AI Models for Anonymization and De-identification of PHI Across Multiple Languages

The rise of chronic diseases and pandemics like COVID-19 has emphasized the need for effective patient data processing while ensuring privacy through anonymization and de-identification of protected health information (PHI). Anonymized data facilitates research without compromising patient confidentiality. This paper introduces expert small AI models developed using the LLM-in-the-loop methodology to meet the demand for domain-specific de-identification NER models. These models overcome the privacy risks associated with large language models (LLMs) used via APIs by eliminating the need to transmit or store sensitive data. More importantly, they consistently outperform LLMs in de-identification tasks, offering superior performance and reliability. Our de-identification NER models, developed in eight languages (English, German, Italian, French, Romanian, Turkish, Spanish, and Arabic) achieved f1-micro score averages of 0.966, 0.975, 0.976, 0.970, 0.964, 0.974, 0.978, and 0.953 respectively. These results establish them as the most accurate healthcare anonymization solutions, surpassing existing small models and even general-purpose LLMs such as GPT-4o. While Part-1 of this series introduced the LLM-in-the-loop methodology for bio-medical document translation, this second paper showcases its success in developing cost-effective expert small NER models in de-identification tasks. Our findings lay the groundwork for future healthcare AI innovations, including biomedical entity and relation extraction, demonstrating the value of specialized models for domain-specific challenges.

  • 3 authors
·
Dec 14, 2024

The P-DESTRE: A Fully Annotated Dataset for Pedestrian Detection, Tracking, Re-Identification and Search from Aerial Devices

Over the last decades, the world has been witnessing growing threats to the security in urban spaces, which has augmented the relevance given to visual surveillance solutions able to detect, track and identify persons of interest in crowds. In particular, unmanned aerial vehicles (UAVs) are a potential tool for this kind of analysis, as they provide a cheap way for data collection, cover large and difficult-to-reach areas, while reducing human staff demands. In this context, all the available datasets are exclusively suitable for the pedestrian re-identification problem, in which the multi-camera views per ID are taken on a single day, and allows the use of clothing appearance features for identification purposes. Accordingly, the main contributions of this paper are two-fold: 1) we announce the UAV-based P-DESTRE dataset, which is the first of its kind to provide consistent ID annotations across multiple days, making it suitable for the extremely challenging problem of person search, i.e., where no clothing information can be reliably used. Apart this feature, the P-DESTRE annotations enable the research on UAV-based pedestrian detection, tracking, re-identification and soft biometric solutions; and 2) we compare the results attained by state-of-the-art pedestrian detection, tracking, reidentification and search techniques in well-known surveillance datasets, to the effectiveness obtained by the same techniques in the P-DESTRE data. Such comparison enables to identify the most problematic data degradation factors of UAV-based data for each task, and can be used as baselines for subsequent advances in this kind of technology. The dataset and the full details of the empirical evaluation carried out are freely available at http://p-destre.di.ubi.pt/.

  • 5 authors
·
Apr 6, 2020

DetReIDX: A Stress-Test Dataset for Real-World UAV-Based Person Recognition

Person reidentification (ReID) technology has been considered to perform relatively well under controlled, ground-level conditions, but it breaks down when deployed in challenging real-world settings. Evidently, this is due to extreme data variability factors such as resolution, viewpoint changes, scale variations, occlusions, and appearance shifts from clothing or session drifts. Moreover, the publicly available data sets do not realistically incorporate such kinds and magnitudes of variability, which limits the progress of this technology. This paper introduces DetReIDX, a large-scale aerial-ground person dataset, that was explicitly designed as a stress test to ReID under real-world conditions. DetReIDX is a multi-session set that includes over 13 million bounding boxes from 509 identities, collected in seven university campuses from three continents, with drone altitudes between 5.8 and 120 meters. More important, as a key novelty, DetReIDX subjects were recorded in (at least) two sessions on different days, with changes in clothing, daylight and location, making it suitable to actually evaluate long-term person ReID. Plus, data were annotated from 16 soft biometric attributes and multitask labels for detection, tracking, ReID, and action recognition. In order to provide empirical evidence of DetReIDX usefulness, we considered the specific tasks of human detection and ReID, where SOTA methods catastrophically degrade performance (up to 80% in detection accuracy and over 70% in Rank-1 ReID) when exposed to DetReIDXs conditions. The dataset, annotations, and official evaluation protocols are publicly available at https://www.it.ubi.pt/DetReIDX/

  • 11 authors
·
May 7, 2025 2

Person Re-identification by Contour Sketch under Moderate Clothing Change

Person re-identification (re-id), the process of matching pedestrian images across different camera views, is an important task in visual surveillance. Substantial development of re-id has recently been observed, and the majority of existing models are largely dependent on color appearance and assume that pedestrians do not change their clothes across camera views. This limitation, however, can be an issue for re-id when tracking a person at different places and at different time if that person (e.g., a criminal suspect) changes his/her clothes, causing most existing methods to fail, since they are heavily relying on color appearance and thus they are inclined to match a person to another person wearing similar clothes. In this work, we call the person re-id under clothing change the "cross-clothes person re-id". In particular, we consider the case when a person only changes his clothes moderately as a first attempt at solving this problem based on visible light images; that is we assume that a person wears clothes of a similar thickness, and thus the shape of a person would not change significantly when the weather does not change substantially within a short period of time. We perform cross-clothes person re-id based on a contour sketch of person image to take advantage of the shape of the human body instead of color information for extracting features that are robust to moderate clothing change. Due to the lack of a large-scale dataset for cross-clothes person re-id, we contribute a new dataset that consists of 33698 images from 221 identities. Our experiments illustrate the challenges of cross-clothes person re-id and demonstrate the effectiveness of our proposed method.

  • 3 authors
·
Feb 6, 2020

Using Degeneracy in the Loss Landscape for Mechanistic Interpretability

Mechanistic Interpretability aims to reverse engineer the algorithms implemented by neural networks by studying their weights and activations. An obstacle to reverse engineering neural networks is that many of the parameters inside a network are not involved in the computation being implemented by the network. These degenerate parameters may obfuscate internal structure. Singular learning theory teaches us that neural network parameterizations are biased towards being more degenerate, and parameterizations with more degeneracy are likely to generalize further. We identify 3 ways that network parameters can be degenerate: linear dependence between activations in a layer; linear dependence between gradients passed back to a layer; ReLUs which fire on the same subset of datapoints. We also present a heuristic argument that modular networks are likely to be more degenerate, and we develop a metric for identifying modules in a network that is based on this argument. We propose that if we can represent a neural network in a way that is invariant to reparameterizations that exploit the degeneracies, then this representation is likely to be more interpretable, and we provide some evidence that such a representation is likely to have sparser interactions. We introduce the Interaction Basis, a tractable technique to obtain a representation that is invariant to degeneracies from linear dependence of activations or Jacobians.

  • 8 authors
·
May 17, 2024

Learning to Purification for Unsupervised Person Re-identification

Unsupervised person re-identification is a challenging and promising task in computer vision. Nowadays unsupervised person re-identification methods have achieved great progress by training with pseudo labels. However, how to purify feature and label noise is less explicitly studied in the unsupervised manner. To purify the feature, we take into account two types of additional features from different local views to enrich the feature representation. The proposed multi-view features are carefully integrated into our cluster contrast learning to leverage more discriminative cues that the global feature easily ignored and biased. To purify the label noise, we propose to take advantage of the knowledge of teacher model in an offline scheme. Specifically, we first train a teacher model from noisy pseudo labels, and then use the teacher model to guide the learning of our student model. In our setting, the student model could converge fast with the supervision of the teacher model thus reduce the interference of noisy labels as the teacher model greatly suffered. After carefully handling the noise and bias in the feature learning, our purification modules are proven to be very effective for unsupervised person re-identification. Extensive experiments on three popular person re-identification datasets demonstrate the superiority of our method. Especially, our approach achieves a state-of-the-art accuracy 85.8\% @mAP and 94.5\% @Rank-1 on the challenging Market-1501 benchmark with ResNet-50 under the fully unsupervised setting. The code will be released.

  • 5 authors
·
Apr 21, 2022

When the signal is in the noise: Exploiting Diffix's Sticky Noise

Anonymized data is highly valuable to both businesses and researchers. A large body of research has however shown the strong limits of the de-identification release-and-forget model, where data is anonymized and shared. This has led to the development of privacy-preserving query-based systems. Based on the idea of "sticky noise", Diffix has been recently proposed as a novel query-based mechanism satisfying alone the EU Article~29 Working Party's definition of anonymization. According to its authors, Diffix adds less noise to answers than solutions based on differential privacy while allowing for an unlimited number of queries. This paper presents a new class of noise-exploitation attacks, exploiting the noise added by the system to infer private information about individuals in the dataset. Our first differential attack uses samples extracted from Diffix in a likelihood ratio test to discriminate between two probability distributions. We show that using this attack against a synthetic best-case dataset allows us to infer private information with 89.4% accuracy using only 5 attributes. Our second cloning attack uses dummy conditions that conditionally strongly affect the output of the query depending on the value of the private attribute. Using this attack on four real-world datasets, we show that we can infer private attributes of at least 93% of the users in the dataset with accuracy between 93.3% and 97.1%, issuing a median of 304 queries per user. We show how to optimize this attack, targeting 55.4% of the users and achieving 91.7% accuracy, using a maximum of only 32 queries per user. Our attacks demonstrate that adding data-dependent noise, as done by Diffix, is not sufficient to prevent inference of private attributes. We furthermore argue that Diffix alone fails to satisfy Art. 29 WP's definition of anonymization. [...]

  • 5 authors
·
Apr 18, 2018