Multiple-Time-Series Clinical Data Processing for Classification With Merging Algorithm and Statistical Measures

lab: an R package for generating analysis-ready data from laboratory records

Background

Electronic health records (EHRs) play a crucial role in healthcare decision-making by giving physicians insights into disease progression and suitable treatment options. Within EHRs, laboratory test results are frequently utilized for predicting disease progression. However, processing laboratory test results often poses challenges due to variations in units and formats. In addition, leveraging the temporal information in EHRs can improve outcomes, prognoses, and diagnosis predication. Nevertheless, the irregular frequency of the data in these records necessitates data preprocessing, which can add complexity to time-series analyses.

Methods

To address these challenges, we developed an open-source R package that facilitates the extraction of temporal information from laboratory records. The proposed lab package generates analysis-ready time series data by segmenting the data into time-series windows and imputing missing values. Moreover, users can map local laboratory codes to the Logical Observation Identifier Names and Codes (LOINC), an international standard. This mapping allows users to incorporate additional information, such as reference ranges and related diseases. Moreover, the reference ranges provided by LOINC enable us to categorize results into normal or abnormal. Finally, the analysis-ready time series data can be further summarized using descriptive statistics and utilized to develop models using machine learning technologies.

Results

Using the lab package, we analyzed data from MIMIC-III, focusing on newborns with patent ductus arteriosus (PDA). We extracted time-series laboratory records and compared the differences in test results between patients with and without 30-day in-hospital mortality. We then identified significant variations in several laboratory test results 7 days after PDA diagnosis. Leveraging the time series-analysis-ready data, we trained a prediction model with the long short-term memory algorithm, achieving an area under the receiver operating characteristic curve of 0.83 for predicting 30-day in-hospital mortality in model training. These findings demonstrate the lab package's effectiveness in analyzing disease progression.

Conclusions

The proposed lab package simplifies and expedites the workflow involved in laboratory records extraction. This tool is particularly valuable in assisting clinical data analysts in overcoming the obstacles associated with heterogeneous and sparse laboratory records.

Harnessing repeated measurements of predictor variables for clinical risk prediction: a review of existing methods

BACKGROUND

Clinical prediction models (CPMs) predict the risk of health outcomes for individual patients. The majority of existing CPMs only harness cross-sectional patient information. Incorporating repeated measurements, such as those stored in electronic health records, into CPMs may provide an opportunity to enhance their performance. However, the number and complexity of methodological approaches available could make it difficult for researchers to explore this opportunity. Our objective was to review the literature and summarise existing approaches for harnessing repeated measurements of predictor variables in CPMs, primarily to make this field more accessible for applied researchers.

METHODS

MEDLINE, Embase and Web of Science were searched for articles reporting the development of a multivariable CPM for individual-level prediction of future binary or time-to-event outcomes and modelling repeated measurements of at least one predictor. Information was extracted on the following: the methodology used, its specific aim, reported advantages and limitations, and software available to apply the method.

RESULTS

The search revealed 217 relevant articles. Seven methodological frameworks were identified: time-dependent covariate modelling, generalised estimating equations, landmark analysis, two-stage modelling, joint-modelling, trajectory classification and machine learning. Each of these frameworks satisfies at least one of three aims: to better represent the predictor-outcome relationship over time, to infer a covariate value at a pre-specified time and to account for the effect of covariate change.

CONCLUSIONS

The applicability of identified methods depends on the motivation for including longitudinal information and the method's compatibility with the clinical context and available patient data, for both model development and risk estimation in practice.

An Optimized HCC Recurrence Prediction Using APO Algorithm Multiple Time Series Clinical Liver Cancer Dataset

The classification of recurrence and non recurrence of Hepato Cellular carcinoma (HCC) outcome after Radio Frequency Ablation therapy is a critical task. Multiple time series clinical liver cancer dataset is collected from different dataset and time interval. A merging algorithm is used to merge all attributes collected from different sources in multiple time periods. In order to preserve the originality of information, statistical measures of each attribute is calculated and considered them as additional attributes for accurate prediction. However the merged dataset is unbalanced, in which, the number of samples from HCC recurrence class is much smaller than from HCC non recurrence. The feature weighting scheme select optimal features and parameter of classifiers are sequentially obtained from multiple iterations which causes higher computation time. In this paper, an efficient sampling approach is proposed using Inverse Random under Sampling (IRUS) to overcome class imbalance issue. IRUS under sample the majority class which creates a number of distinct partitions with a boundary separated minority and majority class samples. Additionally an optimization approach is proposed using Artificial Plant Optimization (APO) algorithm to select optimal features and parameters of classifiers to improve the effectiveness and efficiency of classification. The optimization approach reduces the number of iteration and computation time for feature selection and parameter selection for classifiers which classify the recurrence and non recurrence of HCC. Classify patients with HCC and without HCC based on optimal features and parameters by Support Vector Machine (SVM) and Random Forest(RF) classifiers. Finally, the experimental results are conducted to prove the effectiveness of the proposed method over existing method in terms of accuracy, specificity, sensitivity and balanced accuracy.