Elastic Net Regularized Regression Model Research Articles

The oncologic burden of residual disease in incidental gallbladder cancer: An elastic net regression model to profile high-risk features

IntroductionIncidental Gallbladder Cancer (IGBC) following cholecystectomy constitutes a significant portion of gallbladder cancer diagnoses. Re-exploration is advocated to optimize disease clearance and enhance survival rates. The consistent association of residual disease (RD) with inferior oncologic outcomes prompts a critical examination of re-resection's role as a modifying factor in the natural history of IGBC. MethodsAll patients diagnosed with gallbladder cancer between 2012 and 2022 were included. An elastic net regularized regression model was employed to profile high-risk predictors of RD within the IGBC group. Survival outcomes were assessed based on resection margins and RD. ResultsAmong the 181 patients undergoing re-exploration for IGBC, 133 (73.5 %) harbored RD, while 48 (26.5 %) showed no evidence. The elastic net model, utilizing a selected λ = 0.029, identified six coefficients associated with the risk of RD: aspiration from cholecystectomy (0.141), hepatic tumor origin (1.852), time to re-exploration >8 weeks (1.879), positive margin status (2.575), higher T stage (1.473), and poorly differentiated tumors (2.241). Furthermore, the study revealed a median overall survival of 44 months (CI 38–60) for IGBC patients with no evidence of RD, compared to 31 months (23–42) for those with RD (p < 0.001). ConclusionRe-resection revealed a high incidence of RD (73.5 %), significantly correlating with poorer survival outcomes. The preoperative identification of high-risk features provides a reliable biological disease profile. This aids in strategic preselection of patients who may benefit from re-resection, underscoring the need to consolidate outcomes with tailored chemotherapy for those with unfavorable characteristics.

What causes US equity market sector volatilities during the coronavirus pandemic?

ABSTRACT This paper seeks to identify key variables contributing to sectoral stock market volatilities in the US under the enduring pressure of the COVID-19 pandemic, using a broad array of candidate factors. We adopt a Beta-Skew-t-EGARCH model to capture the time-varying dynamics of the individual sectoral return volatilities. The empirical analysis is performed via an elastic-net regularized regression model. We find that trading volume, volatility of broad US dollar exchange rates, coronavirus infection rates, VIX, Google search trends, US economic policy uncertainty, and the initiation of vaccination programmes are the most common determinants of sectoral volatility.

Global metabolomics revealed deviations from the metabolic aging clock in colorectal cancer patients.

Background: Markers of aging hold promise in the context of colorectal cancer (CRC) care. Utilizing high-resolution metabolomic profiling, we can unveil distinctive age-related patterns that have the potential to predict early CRC development. Our study aims to unearth a panel of aging markers and delve into the metabolomic alterations associated with aging and CRC. Methods: We assembled a serum cohort comprising 5,649 individuals, consisting of 3,002 healthy volunteers, 715 patients diagnosed with colorectal advanced precancerous lesions (APL), and 1,932 CRC patients, to perform a comprehensive metabolomic analysis. Results: We successfully identified unique age-associated patterns across 42 metabolic pathways. Moreover, we established a metabolic aging clock, comprising 9 key metabolites, using an elastic net regularized regression model that accurately estimates chronological age. Notably, we observed significant chronological disparities among the healthy population, APL patients, and CRC patients. By combining the analysis of circulative carcinoembryonic antigen levels with the categorization of individuals into the "hypo" metabolic aging subgroup, our blood test demonstrates the ability to detect APL and CRC with positive predictive values of 68.4% (64.3%, 72.2%) and 21.4% (17.8%, 25.9%), respectively. Conclusions: This innovative approach utilizing our metabolic aging clock holds significant promise for accurately assessing biological age and enhancing our capacity to detect APL and CRC.

Identification of long non-coding RNA signatures for squamous cell carcinomas and adenocarcinomas.

Studies have demonstrated that both squamous cell carcinomas (SCCs) and adenocarcinomas (ACs) possess some common molecular characteristics. Evidence has accumulated to support the theory that long non-coding RNAs (lncRNAs) serve as novel biomarkers and therapeutic targets in complex diseases such as cancer.In this study, we aimed to identify pan lncRNA signatures that are common to squamous cell carcinomas or adenocarcinomas with different tissues of origin. With the aid of elastic-net regularized regression models, a 35-lncRNA pan discriminative signature and an 11-lncRNA pan prognostic signature were identified for squamous cell carcinomas, whereas a 6-lncRNA pan discriminative signature and a 5-lncRNA pan prognostic signature were identified for adenocarcinomas. Among them, many well-known cancer relevant genes such as MALAT1 and PVT1 were included.The identified pan lncRNA lists can help experimental biologists generate research hypotheses and adopt existing treatments for less prevalent cancers. Therefore, these signatures warrant further investigation.

Hypergraph-based image search reranking with elastic net regularized regression

Image search reranking is emerging as an effective technique to refine the text-based image search results using visual information. In this paper, we introduce a novel hypergraph-based image search reranking method that accounts for both relevance and diversity of search results. Namely, the text-based image search results are taken as vertices in a probabilistic regression-based hypergraph model and reranking is formulated as a hypergraph ranking problem with absorbing nodes. More specifically, to discover related samples and characterize the relationships among them, we bring the Elastic Net regularized regression model into the hypergraph construction. Exceeding the conventional hypergraph construction schemes, our scheme is able to describe the high-order relationships and the local manifold structure among visual samples while ensuring the datum-adaptiveness. Afterward, we apply a hypergraph-based ranking with absorbing nodes to ensure a diversified reranking. That is, during the reranking process, previously-ranked samples are transformed into absorbing nodes at each iteration, thereby redundant ones are prevented from receiving high ranking scores. Extensive experiments on real-world data from Flickr suggest our proposed reranking method achieves promising results compared to existing reranking methods.

The impact of deceased donor maintenance on delayed kidney allograft function: A machine learning analysis.

This study evaluated the risk factors for delayed graft function (DGF) in a country where its incidence is high, detailing donor maintenance-related (DMR) variables and using machine learning (ML) methods beyond the traditional regression-based models. A total of 443 brain dead deceased donor kidney transplants (KT) from two Brazilian centers were retrospectively analyzed and the following DMR were evaluated using predictive modeling: arterial blood gas pH, serum sodium, blood glucose, urine output, mean arterial pressure, vasopressors use, and reversed cardiac arrest. Most patients (95.7%) received kidneys from standard criteria donors. The incidence of DGF was 53%. In multivariable logistic regression analysis, DMR variables did not impact on DGF occurrence. In post-hoc analysis including only KT with cold ischemia time<21h (n = 220), urine output in 24h prior to recovery surgery (OR = 0.639, 95%CI 0.444-0.919) and serum sodium (OR = 1.030, 95%CI 1.052-1.379) were risk factors for DGF. Using elastic net regularized regression model and ML analysis (decision tree, neural network and support vector machine), urine output and other DMR variables emerged as DGF predictors: mean arterial pressure, ≥ 1 or high dose vasopressors and blood glucose. Some DMR variables were associated with DGF, suggesting a potential impact of variables reflecting poor clinical and hemodynamic status on the incidence of DGF.

Elastic net regularized regression for time-series analysis of plasma metabolome stability under sub-optimal freezing condition

In this paper, the stability of the plasma metabolome at −20 °C for up to 30 days was evaluated using liquid chromatography-high resolution mass spectrometric metabolomics analysis. To follow the time-series deterioration of the plasma metabolome, the use of an elastic net regularized regression model for the prediction of storage time at −20 °C based on the plasma metabolomic profile, and the selection and ranking of metabolites with high temporal changes was demonstrated using the glmnet package in R. Out of 1229 (positive mode) and 1483 (negative mode) metabolite features, the elastic net model extracted 32 metabolites of interest in both positive and negative modes. L-gamma-glutamyl-L-(iso)leucine (tentative identification) was found to have the highest time-dependent change and significantly increased proportionally to the storage time of plasma at −20 °C (R2 = 0.6378 [positive mode], R2 = 0.7893 [negative mode], p-value < 0.00001). Based on the temporal profiles of the extracted metabolites by the model, results show only minimal deterioration of the plasma metabolome at −20 °C up to 1 month. However, majority of the changes appeared at around 12–15 days of storage. This allows scientists to better plan logistics and storage strategies for samples obtained from low-resource settings, where −80 °C storage is not guaranteed.

Structure-Based Prediction of Anti-infective Drug Concentrations in the Human Lung Epithelial Lining Fluid.

Obtaining pharmacologically relevant exposure levels of antibiotics in the epithelial lining fluid (ELF) is of critical importance to ensure optimal treatment of lung infections. Our objectives were to develop a model for the prediction of the ELF-plasma concentration ratio (EPR) of antibiotics based on their chemical structure descriptors (CSDs). EPR data was obtained by aggregating ELF and plasma concentrations from historical clinical studies investigating antibiotics and associated agents. An elastic net regularized regression model was used to predict EPRs based on a large number of CSDs. The model was tuned using leave-one-drug-out cross validation, and the predictions were further evaluated using a test dataset. EPR data of 56 unique compounds was included. A high degree of variability in EPRs both between- and within drugs was apparent. No trends related to study design or pharmacokinetic factors could be identified. The model predicted 80% of the within-drug variability (R(2) WDV) and 78.6% of drugs were within 3-fold difference from the observations. Key CSDs were related to molecular size and lipophilicity. When predicting EPRs for a test dataset the R(2) WDV was 75%. This model is of relevance to inform dose selection and optimization during antibiotic drug development of agents targeting lung infections.

Assessment and classification of early-stage multiple sclerosis with inertial sensors: comparison against clinical measures of disease state.

A cross-sectional study on patients with early-stage multiple sclerosis (MS) was conducted to examine the reliability of manual and automatic mobility measures derived from shank-mounted inertial sensors during the Timed Up and Go (TUG) test, compared to control subjects. Furthermore, we aimed to determine if disease status [as measured by the Multiple Sclerosis Impact Scale (MSIS-20) and the Expanded Disability Status Score (EDSS)] can be explained by measurements obtained using inertial sensors. We also aimed to determine if patients with early-stage MS could be automatically distinguished from healthy controls subjects, using inertial parameters recorded during the TUG test. The mobility of 38 patients (aged 25-65years, 14M, 24 F), diagnosed with relapsing-remitting MS and 33 healthy controls (14M, 19 F, age 50-65), was assessed using the TUG test, while patients wore inertial sensors on each shank. Reliability analysis showed that 36 of 53 mobility parameters obtained during the TUG showed excellent intrasession reliability, while nine of 53 showed moderate reliability. This compared favorably with the reliability of the mobility parameters in healthy controls. Exploratory regression models of the EDSS and MSIS-20 scales were derived, using mobility parameters and an elastic net procedure in order to determine which mobility parameters influence disease state. A cross-validated elastic net regularized regression model for MSIS-20 yielded a mean square error (MSE) of 1.1 with 10 degrees of freedom (DoF). Similarly, an elastic net regularized regression model for EDSS yielded a cross-validated MSE of 1.3 with 10 DoF. Classification results show that the mobility parameters of participants with early-stage MS could be distinguished from controls with 96.90% accuracy. Results suggest that mobility parameters derived from MS patients while completing the TUG test are reliable, are associated with disease state in MS, and may have utility in screening for early-stage MS.

Quantitative assessment of multiple sclerosis using inertial sensors and the TUG test.

Multiple sclerosis (MS) is a progressive neurological disorder affecting between 2 and 2.5 million people globally. Tests of mobility form part of clinical assessments of MS. Quantitative assessment of mobility using inertial sensors has the potential to provide objective, longitudinal monitoring of disease progression in patients with MS. The mobility of 21 patients (aged 25-59 years, 8 M, 13 F), diagnosed with relapsing-remitting MS was assessed using the Timed up and Go (TUG) test, while patients wore shank-mounted inertial sensors. This exploratory, cross-sectional study aimed to examine the reliability of quantitative measures derived from inertial sensors during the TUG test, in patients with MS. Furthermore, we aimed to determine if disease status (as measured by the Multiple Sclerosis Impact Scale (MSIS-29) and the Expanded Disability Status Score (EDSS)) can be predicted by assessment using a TUG test and inertial sensors. Reliability analysis showed that 32 of 52 inertial sensors parameters obtained during the TUG showed excellent intrasession reliability, while 11 of 52 showed moderate reliability. Using the inertial sensors parameters, regression models of the EDSS and MSIS-29 scales were derived using the elastic net procedure. Using cross validation, an elastic net regularized regression model of MSIS yielded a mean square error (MSE) of 334.6 with 25 degrees of freedom (DoF). Similarly, an elastic net regularized regression model of EDSS yielded a cross-validated MSE of 1.5 with 6 DoF. Results suggest that inertial sensor parameters derived from MS patients while completing the TUG test are reliable and may have utility in assessing disease state as measured using EDSS and MSIS.