Deep-ADCA: Development and Validation of Deep Learning Model for Automated Diagnosis Code Assignment Using Clinical Notes in Electronic Medical Records (original) (raw)
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A deep learning model for the analysis of medical reports in ICD-10 clinical coding task
Proceedings of the Seventh Italian Conference on Computational Linguistics CLiC-it 2020
English. The practice of assigning a uniquely identifiable and easily traceable code to pathology from medical diagnoses is an added value to the current modality of archiving health data collected to build the clinical history of each of us. Unfortunately, the enormous amount of possible pathologies and medical conditions has led to the realization of extremely wide international codifications that are difficult to consult even for a human being. This difficulty makes the practice of annotation of diagnoses with ICD-10 codes very cumbersome and rarely performed. In order to support this operation, a classification model was proposed, able to analyze medical diagnoses written in natural language and automatically assign one or more international reference codes. The model has been evaluated on a dataset released in the Spanish language for the eHealth challenge (CodiEsp) of the international conference CLEF 2020, but it could be extended to any language with latin characters. We proposed a model based on a two-step classification process based on BERT and BiLSTM. Although still far from an accuracy sufficient to do without a licensed physician opinion, the results obtained show the feasibility of the task and are a starting point for future studies in this direction.
2019
Coding diagnosis and procedures in medical records is a crucial process in the healthcare industry, which includes the creation of accurate billings, receiving reimbursements from payers, and creating standardized patient care records. In the United States, Billing and Insurance related activities cost around $471 billion in 2012 which constitutes about 25% of all the U.S hospital spending. In this paper, we report the performance of a natural language processing model that can map clinical notes to medical codes, and predict final diagnosis from unstructured entries of history of present illness, symptoms at the time of admission, etc. Previous studies have demonstrated that deep learning models perform better at such mapping when compared to conventional machine learning models. Therefore, we employed state-of-the-art deep learning method, ULMFiT on the largest emergency department clinical notes dataset MIMIC III which has 1.2M clinical notes to select for the top-10 and top-50 d...
An Empirical Evaluation of Deep Learning for ICD-9 Code Assignment using MIMIC-III Clinical Notes
Computer Methods and Programs in Biomedicine
Background and Objective: Code assignment is of paramount importance in many levels in modern hospitals, from ensuring accurate billing process to creating a valid record of patient care history. However, the coding process is tedious and subjective, and it requires medical coders with extensive training. This study aims to evaluate the performance of deep-learning-based systems to automatically map clinical notes to ICD-9 medical codes. Methods: The evaluations of this research are focused on end-to-end learning methods without manually defined rules. Traditional machine learning algorithms, as well as state-of-the-art deep learning methods such as Recurrent Neural Networks and Convolution Neural Networks, were applied to the Medical Information Mart for Intensive Care (MIMIC-III) dataset. An extensive number of experiments was applied to different settings of the tested algorithm. Results: Findings showed that the deep learning-based methods outperformed other conventional machine learning methods. From our assessment, the best models could predict the top 10 ICD-9 codes with 0.6957 F 1 and 0.8967 accuracy and could estimate the top 10 ICD-9 categories with 0.7233 F 1 and 0.8588 accuracy. Our implementation also outperformed existing work under certain evaluation metrics. Conclusion: A set of standard metrics was utilized in assessing the performance of ICD-9 code assignment on MIMIC-III dataset. All the developed evaluation tools and resources are available online, which can be used as a baseline for further research.
2020
In the United States, 25% or greater than 200 billion dollars of hospital spending accounts for administrative costs that involve services for medical coding and billing. With the increasing number of patient records, manual assignment of the codes performed is overwhelming, time-consuming and error-prone, causing billing errors. Natural language processing can automate the extraction of codes/labels from unstructured clinical notes, which can aid human coders to save time, increase productivity, and verify medical coding errors. Our objective is to identify appropriate diagnosis and procedure codes from clinical notes by performing multi-label classification. We used de-identified data of critical care patients from the MIMIC-III database and subset the data to select the ten (top-10) and fifty (top-50) most common diagnoses and procedures, which covers 47.45% and 74.12% of all admissions respectively. We implemented state-of-the-art Bidirectional Encoder Representations from Trans...
Journal of Digital Health
Financial costs are a major concern in the healthcare system, with medical billing and coding playing a key role in facilitating transactions and financing procedures. Billing involves filing claims with insurance companies and requires scrutiny of clinical summaries and electronic health records to correctly match diagnoses, prescriptions, and procedures to standardized codes. Accuracy in assigning International Classification of Diseases (ICD) codes is critical to proper reimbursement of care. Incorrect codes waste time and resources, and cause administrative and financial problems for hospitals, insurance companies and patients. Manual medical coding is a labor-intensive and error-prone process that creates additional administrative burden and inconvenience for hospitals, insurance companies, and patients. To simplify the process, clinical records are often processed to automatically identify and extract clinical concepts and corresponding ICD codes. Deep learning and natural lan...
JMIR Medical Informatics, 2020
Background The recognition of medical entities from natural language is a ubiquitous problem in the medical field, with applications ranging from medical coding to the analysis of electronic health data for public health. It is, however, a complex task usually requiring human expert intervention, thus making it expansive and time-consuming. Recent advances in artificial intelligence, specifically the rise of deep learning methods, have enabled computers to make efficient decisions on a number of complex problems, with the notable example of neural sequence models and their powerful applications in natural language processing. However, they require a considerable amount of data to learn from, which is typically their main limiting factor. The Centre for Epidemiology on Medical Causes of Death (CépiDc) stores an exhaustive database of death certificates at the French national scale, amounting to several millions of natural language examples provided with their associated human-coded m...
Context of Medical Information Processing System Using Deep Learning and Natural Language Processing
This paper aims to develop and analyze deep learning and natural language processing systems in the context of medical information processing. The amount of data created about patients in the healthcare system is always increasing. The human review of this enormous volume of data derived from numerous sources is expensive and takes a lot of time. Additionally, during a patient visit, doctors write down the patient's medical encounter and send it to nurses and other medical departments for processing. Often, the doctor doesn't have enough time to record every observation made while examining the patient and asking about their medical history which takes time for a medical diagnosis to be made. The manual review of this vast amount of data generated from multiple sources is costly and very time-consuming. It brings huge challenges while attempting to review this data meaningfully. Therefore, the goal of this research is to create a system that will address the aforementioned issues. The suggested method extracts voice data from medical encounters and converts it to text using Deep Learning (DL) and Natural Language Processing (NLP) techniques. More so, the system developed will improve medical intelligence processing by using deep learning to analyze medical datasets and produce results of a diagnosis, assisting medical professionals at various levels in making realistic, intelligent decisions in realtime regarding crucial health issues. The system was designed using the Object-Oriented Analysis and Design Methodology (OOADM), and the user interfaces were put into place utilizing Natural Language Processing techniques, particularly speech recognition and natural language comprehension. Speech recognition allows for the taking of free text notes, which can drastically cut down on the amount of time medical staff spends on labor-in the tensive clinical recording. By extracting different pieces of data for medical diagnosis and producing results in a matter of seconds, a deep learning algorithm demonstrates a significant capacity to construct clinical decision support systems. The system's results demonstrate that the deep learning algorithm enabled medical intelligence to be 96.7 percent accurate.
Incorporating medical code descriptions for diagnosis prediction in healthcare
BMC Medical Informatics and Decision Making
Background Diagnosis aims to predict the future health status of patients according to their historical electronic health records (EHR), which is an important yet challenging task in healthcare informatics. Existing diagnosis prediction approaches mainly employ recurrent neural networks (RNN) with attention mechanisms to make predictions. However, these approaches ignore the importance of code descriptions, i.e., the medical definitions of diagnosis codes. We believe that taking diagnosis code descriptions into account can help the state-of-the-art models not only to learn meaning code representations, but also to improve the predictive performance, especially when the EHR data are insufficient. Methods We propose a simple, but general diagnosis prediction framework, which includes two basic components: diagnosis code embedding and predictive model. To learn the interpretable code embeddings, we apply convolutional neural networks (CNN) to model medical descriptions of diagnosis cod...
Convolutional Neural Networks for Medical Diagnosis from Admission Notes
ArXiv, 2017
Objective Develop an automatic diagnostic system which only uses textual admission information from Electronic Health Records (EHRs) and assist clinicians with a timely and statistically proved decision tool. The hope is that the tool can be used to reduce mis-diagnosis. Materials and Methods We use the real-world clinical notes from MIMIC-III, a freely available dataset consistsing of clinical data of more than forty thousand patients who stayed in intensive care units of the Beth Israel Deaconess Medical Center between 2001 and 2012 (Johnson et al., 2016). We proposed a Convolutional Neural Network model to learn semantic features from unstructured textual input and automatically predict primary discharge diagnosis. Results The proposed model achieved an overall 96.11% accuracy and 80.48% weighted F1 score values on 10 most frequent disease classes, significantly outperforming four strong baseline models by at least 12.7% in weighted F1 score. Discussion Experimental results imply that the CNN model is suitable for supporting diagnosis decision making in the presence of complex, noisy and unstructured clinical data while at the same time using fewer layers and parameters that other traditional Deep Network models. Conclusion Our model demonstrated capability of representing complex medical meaningful features from unstructured clinical notes and prediction power for commonly misdiagnosed frequent diseases. It can use easily adopted in clinical setting to provide timely and statistically proved decision support.
A study of Machine Learning models for Clinical Coding of Medical Reports at CodiEsp 2020
2020
The task of identifying one or more diseases associated with a patient’s clinical condition is often very complex, even for doctors and specialists. This process is usually time-consuming and has to take into account different aspects of what has occurred, including symptoms elicited and previous healthcare situations. The medical diagnosis is often provided to patients in the form of written paper without any correlation with a national or international standard. Even if the WHO (World Health Organization) released the ICD10 international glossary of diseases, almost no doctor has enough time to manually associate the patient’s clinical history with international codes. The CodiEsp task at CLEF 2020 addressed this issue by proposing the development of an automatic system to deal with this task. Our solution investigated different machine learning strategies in order to identify an approach to face that challenge. The main outcomes of the experiments showed that a strategy based on ...