128 research outputs found

    Clinical Decision Support System for Unani Medicine Practitioners

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    Like other fields of Traditional Medicines, Unani Medicines have been found as an effective medical practice for ages. It is still widely used in the subcontinent, particularly in Pakistan and India. However, Unani Medicines Practitioners are lacking modern IT applications in their everyday clinical practices. An Online Clinical Decision Support System may address this challenge to assist apprentice Unani Medicines practitioners in their diagnostic processes. The proposed system provides a web-based interface to enter the patient's symptoms, which are then automatically analyzed by our system to generate a list of probable diseases. The system allows practitioners to choose the most likely disease and inform patients about the associated treatment options remotely. The system consists of three modules: an Online Clinical Decision Support System, an Artificial Intelligence Inference Engine, and a comprehensive Unani Medicines Database. The system employs advanced AI techniques such as Decision Trees, Deep Learning, and Natural Language Processing. For system development, the project team used a technology stack that includes React, FastAPI, and MySQL. Data and functionality of the application is exposed using APIs for integration and extension with similar domain applications. The novelty of the project is that it addresses the challenge of diagnosing diseases accurately and efficiently in the context of Unani Medicines principles. By leveraging the power of technology, the proposed Clinical Decision Support System has the potential to ease access to healthcare services and information, reduce cost, boost practitioner and patient satisfaction, improve speed and accuracy of the diagnostic process, and provide effective treatments remotely. The application will be useful for Unani Medicines Practitioners, Patients, Government Drug Regulators, Software Developers, and Medical Researchers.Comment: 59 pages, 11 figures, Computer Science Bachelor's Thesis on use of Artificial Intelligence in Clinical Decision Support System for Unani Medicine

    Exploration and adaptation of large language models for specialized domains

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    Large language models have transformed the field of natural language processing (NLP). Their improved performance on various NLP benchmarks makes them a promising tool—also for the application in specialized domains. Such domains are characterized by highly trained professionals with particular domain expertise. Since these experts are rare, improving the efficiency of their work with automated systems is especially desirable. However, domain-specific text resources hold various challenges for NLP systems. These challenges include distinct language, noisy and scarce data, and a high level of variation. Further, specialized domains present an increased need for transparent systems since they are often applied in high stakes settings. In this dissertation, we examine whether large language models (LLMs) can overcome some of these challenges and propose methods to effectively adapt them to domain-specific requirements. We first investigate the inner workings and abilities of LLMs and show how they can fill the gaps that are present in previous NLP algorithms for specialized domains. To this end, we explore the sources of errors produced by earlier systems to identify which of them can be addressed by using LLMs. Following this, we take a closer look at how information is processed within Transformer-based LLMs to better understand their capabilities. We find that their layers encode different dimensions of the input text. Here, the contextual vector representation, and the general language knowledge learned during pre-training are especially beneficial for solving complex and multi-step tasks common in specialized domains. Following this exploration, we propose solutions for further adapting LLMs to the requirements of domain-specific tasks. We focus on the clinical domain, which incorporates many typical challenges found in specialized domains. We show how to improve generalization by integrating different domain-specific resources into our models. We further analyze the behavior of the produced models and propose a behavioral testing framework that can serve as a tool for communication with domain experts. Finally, we present an approach for incorporating the benefits of LLMs while fulfilling requirements such as interpretability and modularity. The presented solutions show improvements in performance on benchmark datasets and in manually conducted analyses with medical professionals. Our work provides both new insights into the inner workings of pre-trained language models as well as multiple adaptation methods showing that LLMs can be an effective tool for NLP in specialized domains

    Using machine learning for automated de-identification and clinical coding of free text data in electronic medical records

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    The widespread adoption of Electronic Medical Records (EMRs) in hospitals continues to increase the amount of patient data that are digitally stored. Although the primary use of the EMR is to support patient care by making all relevant information accessible, governments and health organisations are looking for ways to unleash the potential of these data for secondary purposes, including clinical research, disease surveillance and automation of healthcare processes and workflows. EMRs include large quantities of free text documents that contain valuable information. The greatest challenges in using the free text data in EMRs include the removal of personally identifiable information and the extraction of relevant information for specific tasks such as clinical coding. Machine learning-based automated approaches can potentially address these challenges. This thesis aims to explore and improve the performance of machine learning models for automated de-identification and clinical coding of free text data in EMRs, as captured in hospital discharge summaries, and facilitate the applications of these approaches in real-world use cases. It does so by 1) implementing an end-to-end de-identification framework using an ensemble of deep learning models; 2) developing a web-based system for de-identification of free text (DEFT) with an interactive learning loop; 3) proposing and implementing a hierarchical label-wise attention transformer model (HiLAT) for explainable International Classification of Diseases (ICD) coding; and 4) investigating the use of extreme multi-label long text transformer-based models for automated ICD coding. The key findings include: 1) An end-to-end framework using an ensemble of deep learning base-models achieved excellent performance on the de-identification task. 2) A new web-based de-identification software system (DEFT) can be readily and easily adopted by data custodians and researchers to perform de-identification of free text in EMRs. 3) A novel domain-specific transformer-based model (HiLAT) achieved state-of-the-art (SOTA) results for predicting ICD codes on a Medical Information Mart for Intensive Care (MIMIC-III) dataset comprising the discharge summaries (n=12,808) that are coded with at least one of the most 50 frequent diagnosis and procedure codes. In addition, the label-wise attention scores for the tokens in the discharge summary presented a potential explainability tool for checking the face validity of ICD code predictions. 4) An optimised transformer-based model, PLM-ICD, achieved the latest SOTA results for ICD coding on all the discharge summaries of the MIMIC-III dataset (n=59,652). The segmentation method, which split the long text consecutively into multiple small chunks, addressed the problem of applying transformer-based models to long text datasets. However, using transformer-based models on extremely large label sets needs further research. These findings demonstrate that the de-identification and clinical coding tasks can benefit from the application of machine learning approaches, present practical tools for implementing these approaches, and highlight priorities for further research

    Cyber Threat Intelligence based Holistic Risk Quantification and Management

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    Non-communicable Diseases, Big Data and Artificial Intelligence

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    This reprint includes 15 articles in the field of non-communicable Diseases, big data, and artificial intelligence, overviewing the most recent advances in the field of AI and their application potential in 3P medicine

    HEALTH OUTCOME PATHWAY PREDICTION. A GRAPH-BASED FRAMEWORK

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    This dissertation is part of the project FrailCare.AI, which aims to detect frailty in the elderly Portuguese population in order to optimize the SNS24 (telemonitoring) service, with the goal of suggesting health pathways to reduce the patients frailty. Frailty can be defined as the condition of being weak and delicate which normally increases with age and is the consequence of several health and non-health related factors. A patient health journey is recorded in Eletronic Health Record (EHR), which are rich but sparse, noisy and multi-modal sources of truth. These can be used to train predictive models to predict future health states, where frailty is just one of them. In this work, due to lack of data access we pivoted our focus to phenotype prediction, that is, predicting diagnosis. What is more, we tackle the problem of data-insufficiency and class imbalance (e.g. rare diseases and other infrequent occurrences in the training data) by integrating standardized healthcare ontologies within graph neural networks. We study the broad task of phenotype prediction, multi-task scenarios and as well few-shot scenarios - which is when a class rarely occurs in the training set. Furthermore, during the development of this work we detect some reproducibility issues in related literature which we detail, and also open-source all of our implementations introduding a framework to aid the development of similar systems.A presente dissertação insere-se no projecto FrailCare.AI, que visa detectar a fragilidade da população idosa portuguesa com o objectivo de optimizar o serviço de telemonitoriza- ção do Sistema Nacional de Saúde Português (SNS24), e também sugerir acções a tomar para reduzir a fragilidade dos doentes. A fragilidade é uma condição de risco composta por multiplos fatores. Hoje em dia, grande parte da história clinica de cada utente é gravada digitalmente. Estes dados diversos e vastos podem ser usados treinar modelos preditivos cujo objectivo é prever futuros estados de saúde, sendo que fragilidade é só um deles. Devido à falta de accesso a dados, alteramos a tarefa principal deste trabalho para previsão de diágnosticos, onde exploramos o problema de insuficiência de dados e dese- quilíbrio de classes (por exemplo, doenças raras e outras ocorrências pouco frequentes nos dados de treino), integrando ontologias de conceitos médicos por meio de redes neu- ronais de gráfos. Exploramos também outras tarefas e o impacto que elas têm entre si. Para além disso, durante o desenvolvimento desta dissertação identificamos questões a nivel de reproducibilidade da literatura estudada, onde detalhamos e implementamos os conceitos em falta. Com o objectivo de reproducibilidade em mente, nós libertamos o nosso código, introduzindo um biblioteca que permite desenvlver sistemas semelhantes ao nosso
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