Combining Structured and Unstructured Data in Electronic Health Record for Readmission Prediction via Deep Learning

With the aid of statistical learning tools nowadays, a variety of clinical prediction tasks can be examined and modeled in a quantitative way. Predicting hospital readmission probability is among one of the most significant tasks in that it provides a good indication of the healthcare cost and a patient's health condition. Thus, in this study, we strive to build up a quantitative prediction model for readmission prediction by utilizing both structured data and unstructured text data from a patient's Electronic Health Records (EHR). In the past, a variety of studies focused on using only structured categorical or numerical data such as lab tests and Heart Failure Signs to perform clinical risk prediction tasks, while recently, with the help of deep learning models, people started to use Natural Language Processing techniques to process unstructured patient's text data, as it contains richer information. However, with the belief that both structured and unstructured data can play significant role in predicting readmission, our research will focus on developing deep learning methods to combine the two types of data together in an efficient way, such that the predicting performance will exceed those of the previous models.No embargoAcademic Major: Computer Science and Engineerin

Interpretable Multi-Task Deep Neural Networks for Dynamic Predictions of Postoperative Complications

Accurate prediction of postoperative complications can inform shared decisions between patients and surgeons regarding the appropriateness of surgery, preoperative risk-reduction strategies, and postoperative resource use. Traditional predictive analytic tools are hindered by suboptimal performance and usability. We hypothesized that novel deep learning techniques would outperform logistic regression models in predicting postoperative complications. In a single-center longitudinal cohort of 43,943 adult patients undergoing 52,529 major inpatient surgeries, deep learning yielded greater discrimination than logistic regression for all nine complications. Predictive performance was strongest when leveraging the full spectrum of preoperative and intraoperative physiologic time-series electronic health record data. A single multi-task deep learning model yielded greater performance than separate models trained on individual complications. Integrated gradients interpretability mechanisms demonstrated the substantial importance of missing data. Interpretable, multi-task deep neural networks made accurate, patient-level predictions that harbor the potential to augment surgical decision-making

A comparative analysis of multi-level computer-assisted decision making systems for traumatic injuries

<p>Abstract</p> <p>Background</p> <p>This paper focuses on the creation of a predictive computer-assisted decision making system for traumatic injury using machine learning algorithms. Trauma experts must make several difficult decisions based on a large number of patient attributes, usually in a short period of time. The aim is to compare the existing machine learning methods available for medical informatics, and develop reliable, rule-based computer-assisted decision-making systems that provide recommendations for the course of treatment for new patients, based on previously seen cases in trauma databases. Datasets of traumatic brain injury (TBI) patients are used to train and test the decision making algorithm. The work is also applicable to patients with traumatic pelvic injuries.</p> <p>Methods</p> <p>Decision-making rules are created by processing patterns discovered in the datasets, using machine learning techniques. More specifically, CART and C4.5 are used, as they provide grammatical expressions of knowledge extracted by applying logical operations to the available features. The resulting rule sets are tested against other machine learning methods, including AdaBoost and SVM. The rule creation algorithm is applied to multiple datasets, both with and without prior filtering to discover significant variables. This filtering is performed via logistic regression prior to the rule discovery process.</p> <p>Results</p> <p>For survival prediction using all variables, CART outperformed the other machine learning methods. When using only significant variables, neural networks performed best. A reliable rule-base was generated using combined C4.5/CART. The average predictive rule performance was 82% when using all variables, and approximately 84% when using significant variables only. The average performance of the combined C4.5 and CART system using significant variables was 89.7% in predicting the exact outcome (home or rehabilitation), and 93.1% in predicting the ICU length of stay for airlifted TBI patients.</p> <p>Conclusion</p> <p>This study creates an efficient computer-aided rule-based system that can be employed in decision making in TBI cases. The rule-bases apply methods that combine CART and C4.5 with logistic regression to improve rule performance and quality. For final outcome prediction for TBI cases, the resulting rule-bases outperform systems that utilize all available variables.</p

Extending Relational Query Processing with ML Inference

The broadening adoption of machine learning in the enterprise is increasing the pressure for strict governance and cost-effective performance, in particular for the common and consequential steps of model storage and inference. The RDBMS provides a natural starting point, given its mature infrastructure for fast data access and processing, along with support for enterprise features (e.g., encryption, auditing, high-availability). To take advantage of all of the above, we need to address a key concern: Can in-RDBMS scoring of ML models match (outperform?) the performance of dedicated frameworks? We answer the above positively by building Raven, a system that leverages native integration of ML runtimes (i.e., ONNX Runtime) deep within SQL Server, and a unified intermediate representation (IR) to enable advanced cross-optimizations between ML and DB operators. In this optimization space, we discover the most exciting research opportunities that combine DB/Compiler/ML thinking. Our initial evaluation on real data demonstrates performance gains of up to 5.5x from the native integration of ML in SQL Server, and up to 24x from cross-optimizations--we will demonstrate Raven live during the conference talk

Deep Learning in Cardiology

The medical field is creating large amount of data that physicians are unable to decipher and use efficiently. Moreover, rule-based expert systems are inefficient in solving complicated medical tasks or for creating insights using big data. Deep learning has emerged as a more accurate and effective technology in a wide range of medical problems such as diagnosis, prediction and intervention. Deep learning is a representation learning method that consists of layers that transform the data non-linearly, thus, revealing hierarchical relationships and structures. In this review we survey deep learning application papers that use structured data, signal and imaging modalities from cardiology. We discuss the advantages and limitations of applying deep learning in cardiology that also apply in medicine in general, while proposing certain directions as the most viable for clinical use.Comment: 27 pages, 2 figures, 10 table

Development of machine learning schemes for use in non-invasive and continuous patient health monitoring

Stephanie Baker developed machine learning schemes for the non-invasive and continuous measurement of blood pressure and respiratory rate from heart activity waveforms. She also constructed machine learning models for mortality risk assessment from vital sign variations. This research contributes several tools that offer significant advancements in patient monitoring and wearable healthcare

PREDICTION OF SEPSIS DISEASE BY ARTIFICIAL NEURAL NETWORKS

Sepsis is a fatal condition, which affects at least 26 million people in the world every year that is resulted by an infection. For every 100,000 people, sepsis is seen in 149-240 of them and it has a mortality rate of 30%. The presence of infection in the patient is determined in order to diagnose the sepsis disease. Organ dysfunctions associated with an infection is diagnosed as sepsis. With the increased usage of artificial intelligence in the field of medicine, the early prediction and treatment of many diseases are provided with these methods. Considering the learning, reasoning and decision making abilities of artificial neural networks, which are the sub field of artificial intelligence are inferred to be used in predicting early stages of sepsis disease and determining the sepsis level is assessed. In this study, it is aimed to help sepsis diagnosis by using multi-layered artificial neural network.In construction of artificial neural network model, feed forward back propagation network structure and Levenberg-Marquardt training algorithm were used. The input and output variables of the model were the parameters which doctors use to diagnose the sepsis disease and determine the level of sepsis. The proposed method aims to provide an alternative prediction model for the early detection of sepsis disease

Clinical Outcome Prediction from Admission Notes using Self-Supervised Knowledge Integration

Outcome prediction from clinical text can prevent doctors from overlooking possible risks and help hospitals to plan capacities. We simulate patients at admission time, when decision support can be especially valuable, and contribute a novel admission to discharge task with four common outcome prediction targets: Diagnoses at discharge, procedures performed, in-hospital mortality and length-of-stay prediction. The ideal system should infer outcomes based on symptoms, pre-conditions and risk factors of a patient. We evaluate the effectiveness of language models to handle this scenario and propose clinical outcome pre-training to integrate knowledge about patient outcomes from multiple public sources. We further present a simple method to incorporate ICD code hierarchy into the models. We show that our approach improves performance on the outcome tasks against several baselines. A detailed analysis reveals further strengths of the model, including transferability, but also weaknesses such as handling of vital values and inconsistencies in the underlying data.Comment: EACL 202

Ensembling Neural Networks for Improved Prediction and Privacy in Early Diagnosis of Sepsis

Ensembling neural networks is a long-standing technique for improving the generalization error of neural networks by combining networks with orthogonal properties via a committee decision. We show that this technique is an ideal fit for machine learning on medical data: First, ensembles are amenable to parallel and asynchronous learning, thus enabling efficient training of patient-specific component neural networks. Second, building on the idea of minimizing generalization error by selecting uncorrelated patient-specific networks, we show that one can build an ensemble of a few selected patient-specific models that outperforms a single model trained on much larger pooled datasets. Third, the non-iterative ensemble combination step is an optimal low-dimensional entry point to apply output perturbation to guarantee the privacy of the patient-specific networks. We exemplify our framework of differentially private ensembles on the task of early prediction of sepsis, using real-life intensive care unit data labeled by clinical experts.Comment: Accepted at MLHC 202

Preserving the knowledge of long clinical texts using aggregated ensembles of large language models

Clinical texts, such as admission notes, discharge summaries, and progress notes, contain rich and valuable information that can be used for various clinical outcome prediction tasks. However, applying large language models, such as BERT-based models, to clinical texts poses two major challenges: the limitation of input length and the diversity of data sources. This paper proposes a novel method to preserve the knowledge of long clinical texts using aggregated ensembles of large language models. Unlike previous studies which use model ensembling or text aggregation methods separately, we combine ensemble learning with text aggregation and train multiple large language models on two clinical outcome tasks: mortality prediction and length of stay prediction. We show that our method can achieve better results than baselines, ensembling, and aggregation individually, and can improve the performance of large language models while handling long inputs and diverse datasets. We conduct extensive experiments on the admission notes from the MIMIC-III clinical database by combining multiple unstructured and high-dimensional datasets, demonstrating our method's effectiveness and superiority over existing approaches. We also provide a comprehensive analysis and discussion of our results, highlighting our method's applications and limitations for future research in the domain of clinical healthcare. The results and analysis of this study is supportive of our method assisting in clinical healthcare systems by enabling clinical decision-making with robust performance overcoming the challenges of long text inputs and varied datasets.Comment: 17 pages, 4 figures, 4 tables, 9 equations and 1 algorith