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The objective of this study is to address the critical issue of de-identification of clinical reports in order to allow access to data for research purposes, while ensuring patient privacy. The study highlights the difficulties faced in sharing tools and resources in this domain and presents the experience of the Greater Paris University Hospitals (AP-HP) in implementing a systematic pseudonymization of text documents from its Clinical Data Warehouse. We annotated a corpus of clinical documents according to 12 types of identifying entities, and built a hybrid system, merging the results of a deep learning model as well as manual rules. Our results show an overall performance of 0.99 of F1-score. We discuss implementation choices and present experiments to better understand the effort involved in such a task, including dataset size, document types, language models, or rule addition. We share guidelines and code under a 3-Clause BSD license.

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 Processing 是一門開源編程語言和與之配套的集成開發環境(IDE)的名稱。Processing 在電子藝術和視覺設計社區被用來教授編程基礎,并運用于大量的新媒體和互動藝術作品中。

[Background] The MVP concept has influenced the way in which development teams apply Software Engineering practices. However, the overall understanding of this influence of MVPs on SE practices is still poor. [Objective] Our goal is to characterize the publication landscape on practices that have been used in the context of software MVPs and to gather practitioner insights on the identified practices. [Method] We conducted a systematic mapping study and discussed its results in two focus groups sessions involving twelve industry practitioners that extensively use MVPs in their projects to capture their perceptions on the findings of the mapping study. [Results] We identified 33 papers published between 2013 and 2020 and observed some trends related to MVP ideation and evaluation practices. For instance, regarding ideation, we found six different approaches and mainly informal end-user involvement practices. Regarding evaluation, there is an emphasis on end-user validations based on practices such as usability tests, A/B testing, and usage data analysis. However, there is still limited research related to MVP technical feasibility assessment and effort estimation. Practitioners of the focus group sessions reinforced the confidence in our results regarding ideation and evaluation practices, being aware of most of the identified practices. They also reported how they deal with the technical feasibility assessments and effort estimation in practice. [Conclusion] Our analysis suggests that there are opportunities for solution proposals and evaluation studies to address literature gaps concerning technical feasibility assessment and effort estimation. Overall, more effort needs to be invested into empirically evaluating the existing MVP-related practices.

Introduction: The Canadian Guidelines recommend physical activity for overall health benefits, including cognitive, emotional, functional, and physical health. However, traditional research methods are inefficient and outdated. This paper aims to guide researchers in enhancing their research methods using software development kits and wearable smart devices. Methods: A generic model application was transformed into a research-based mobile application based on the UCLA researchers who collaborated with Apple. First, the research question and goals were identified. Then, three open-source software development kits (SDKs) were used to modify the generic model into the desired application. ResearchKit was used for informed consent, surveys, and active tasks. CareKit was the protocol manager to create participant protocols and track progress. Finally, HealthKit was used to access and share health-related data. The content expert evaluated the application, and the participant experience was optimized for easy use. The collected health-related data were analyzed to identify any significant findings. Results: Wearable health devices offer a convenient and non-invasive way to monitor and track health-related information. Conclusion: Leveraging the data provided by wearable devices, researchers can gain insights into the effectiveness of interventions and inform the development of evidence-based physical activity guidelines. The use of software development kits and wearable devices can enhance research methods and provide valuable insights into overall health benefits.

This paper describes the results of SemEval 2023 task 7 -- Multi-Evidence Natural Language Inference for Clinical Trial Data (NLI4CT) -- consisting of 2 tasks, a Natural Language Inference (NLI) task, and an evidence selection task on clinical trial data. The proposed challenges require multi-hop biomedical and numerical reasoning, which are of significant importance to the development of systems capable of large-scale interpretation and retrieval of medical evidence, to provide personalized evidence-based care. Task 1, the entailment task, received 643 submissions from 40 participants, and Task 2, the evidence selection task, received 364 submissions from 23 participants. The tasks are challenging, with the majority of submitted systems failing to significantly outperform the majority class baseline on the entailment task, and we observe significantly better performance on the evidence selection task than on the entailment task. Increasing the number of model parameters leads to a direct increase in performance, far more significant than the effect of biomedical pre-training. Future works could explore the limitations of large models for generalization and numerical inference, and investigate methods to augment clinical datasets to allow for more rigorous testing and to facilitate fine-tuning. We envisage that the dataset, models, and results of this task will be useful to the biomedical NLI and evidence retrieval communities. The dataset, competition leaderboard, and website are publicly available.

Impaired cardiac function has been described as a frequent complication of COVID-19-related pneumonia. To investigate possible underlying mechanisms, we represented the cardiovascular system by means of a lumped-parameter 0D mathematical model. The model was calibrated using clinical data, recorded in 58 patients hospitalized for COVID-19-related pneumonia, to make it patient-specific and to compute model outputs of clinical interest related to the cardiocirculatory system. We assessed, for each patient with a successful calibration, the statistical reliability of model outputs estimating the uncertainty intervals. Then, we performed a statistical analysis to compare healthy ranges and mean values (over patients) of reliable model outputs to determine which were significantly altered in COVID-19-related pneumonia. Our results showed significant increases in right ventricular systolic pressure, diastolic and mean pulmonary arterial pressure, and capillary wedge pressure. Instead, physical quantities related to the systemic circulation were not significantly altered. Remarkably, statistical analyses made on raw clinical data, without the support of a mathematical model, were unable to detect the effects of COVID-19-related pneumonia, thus suggesting that the use of a calibrated 0D mathematical model to describe the cardiocirculatory system is an effective tool to investigate the impairments of the cardiocirculatory system associated with COVID-19.

We propose a Bayesian model selection approach that allows medical practitioners to select among predictor variables while taking their respective costs into account. Medical procedures almost always incur costs in time and/or money. These costs might exceed their usefulness for modeling the outcome of interest. We develop Bayesian model selection that uses flexible model priors to penalize costly predictors a priori and select a subset of predictors useful relative to their costs. Our approach (i) gives the practitioner control over the magnitude of cost penalization, (ii) enables the prior to scale well with sample size, and (iii) enables the creation of our proposed inclusion path visualization, which can be used to make decisions about individual candidate predictors using both probabilistic and visual tools. We demonstrate the effectiveness of our inclusion path approach and the importance of being able to adjust the magnitude of the prior's cost penalization through a dataset pertaining to heart disease diagnosis in patients at the Cleveland Clinic Foundation, where several candidate predictors with various costs were recorded for patients, and through simulated data.

Driven by the need for larger and more diverse datasets to pre-train and fine-tune increasingly complex machine learning models, the number of datasets is rapidly growing. audb is an open-source Python library that supports versioning and documentation of audio datasets. It aims to provide a standardized and simple user-interface to publish, maintain, and access the annotations and audio files of a dataset. To efficiently store the data on a server, audb automatically resolves dependencies between versions of a dataset and only uploads newly added or altered files when a new version is published. The library supports partial loading of a dataset and local caching for fast access. audb is a lightweight library and can be interfaced from any machine learning library. It supports the management of datasets on a single PC, within a university or company, or within a whole research community.

This article provides an overview of the importance of requirements gathering in secure software development. It explains the crucial role of Requirements Engineers in defining and understanding the customer's needs and desires, as well as their responsibilities in liaising with the development team. The article also covers various software development life cycles, such as waterfall, spiral, and agile models, and their advantages and disadvantages. Additionally, it explains the importance of domain knowledge and stakeholder-driven elicitation in identifying system goals and firm requirements. The article emphasizes the need to mitigate the risks of vagueness and ambiguity early on and provides techniques for evaluating, negotiating, and prioritizing requirements. Finally, it discusses the importance of turning these requirements into complete, concise, and consistent documents using natural. Overall, this article highlights the critical role of requirements gathering in creating secure and successful software products that meet the customer's needs and expectations.

In pace with developments in the research field of artificial intelligence, knowledge graphs (KGs) have attracted a surge of interest from both academia and industry. As a representation of semantic relations between entities, KGs have proven to be particularly relevant for natural language processing (NLP), experiencing a rapid spread and wide adoption within recent years. Given the increasing amount of research work in this area, several KG-related approaches have been surveyed in the NLP research community. However, a comprehensive study that categorizes established topics and reviews the maturity of individual research streams remains absent to this day. Contributing to closing this gap, we systematically analyzed 507 papers from the literature on KGs in NLP. Our survey encompasses a multifaceted review of tasks, research types, and contributions. As a result, we present a structured overview of the research landscape, provide a taxonomy of tasks, summarize our findings, and highlight directions for future work.

This paper surveys and organizes research works in a new paradigm in natural language processing, which we dub "prompt-based learning". Unlike traditional supervised learning, which trains a model to take in an input x and predict an output y as P(y|x), prompt-based learning is based on language models that model the probability of text directly. To use these models to perform prediction tasks, the original input x is modified using a template into a textual string prompt x' that has some unfilled slots, and then the language model is used to probabilistically fill the unfilled information to obtain a final string x, from which the final output y can be derived. This framework is powerful and attractive for a number of reasons: it allows the language model to be pre-trained on massive amounts of raw text, and by defining a new prompting function the model is able to perform few-shot or even zero-shot learning, adapting to new scenarios with few or no labeled data. In this paper we introduce the basics of this promising paradigm, describe a unified set of mathematical notations that can cover a wide variety of existing work, and organize existing work along several dimensions, e.g.the choice of pre-trained models, prompts, and tuning strategies. To make the field more accessible to interested beginners, we not only make a systematic review of existing works and a highly structured typology of prompt-based concepts, but also release other resources, e.g., a website //pretrain.nlpedia.ai/ including constantly-updated survey, and paperlist.

Recent years have seen important advances in the quality of state-of-the-art models, but this has come at the expense of models becoming less interpretable. This survey presents an overview of the current state of Explainable AI (XAI), considered within the domain of Natural Language Processing (NLP). We discuss the main categorization of explanations, as well as the various ways explanations can be arrived at and visualized. We detail the operations and explainability techniques currently available for generating explanations for NLP model predictions, to serve as a resource for model developers in the community. Finally, we point out the current gaps and encourage directions for future work in this important research area.

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