Optimizing area under the ROC curve using semi-supervised learning

Machine Learning Models for Predicting Bioavailability of Traditional and Emerging Aromatic Contaminants in Plant Roots

To predict the behavior of aromatic contaminants (ACs) in complex soil-plant systems, this study developed machine learning (ML) models to estimate the root concentration factor (RCF) of both traditional (e.g., polycyclic aromatic hydrocarbons, polychlorinated biphenyls) and emerging ACs (e.g., phthalate acid esters, aryl organophosphate esters). Four ML algorithms were employed, trained on a unified RCF dataset comprising 878 data points, covering 6 features of soil-plant cultivation systems and 98 molecular descriptors of 55 chemicals, including 29 emerging ACs. The gradient-boosted regression tree (GBRT) model demonstrated strong predictive performance, with a coefficient of determination (R2) of 0.75, a mean absolute error (MAE) of 0.11, and a root mean square error (RMSE) of 0.22, as validated by five-fold cross-validation. Multiple explanatory analyses highlighted the significance of soil organic matter (SOM), plant protein and lipid content, exposure time, and molecular descriptors related to electronegativity distribution pattern (GATS8e) and double-ring structure (fr_bicyclic). An increase in SOM was found to decrease the overall RCF, while other variables showed strong correlations within specific ranges. This GBRT model provides an important tool for assessing the environmental behaviors of ACs in soil-plant systems, thereby supporting further investigations into their ecological and human exposure risks.

NCAPD2 serves as a potential prognostic biomarker for lung adenocarcinoma and promotes cell proliferation, migration, invasion and cell cycle in vitro

Objectives

The pro-oncogenic effects of NCAPD2 have been extensively studied across various tumor types; however, its precise role within the context of lung adenocarcinoma (LUAD) remains elusive. This study aims to elucidate the biological functions of NCAPD2 in LUAD and unravel the underlying mechanistic pathways.

Methods

Utilizing bioinformatics methodologies, we explored the differential expression of NCAPD2 between normal and tumor samples, along with its correlations with clinical-pathological characteristics, survival prognosis, and immune infiltration.

Results

In the TCGA-LUAD dataset, tumor samples demonstrated significantly elevated levels of NCAPD2 expression compared to normal samples (p < 0.001). Clinically, higher NCAPD2 expression was notably associated with advanced T, N, and M stages, pathologic stage, gender, smoking status, and diminished overall survival (OS). Moreover, differentially expressed genes (DEGs) associated with NCAPD2 were predominantly enriched in pathways related to cell division. Immune infiltration analysis revealed that NCAPD2 expression levels were linked to the infiltration of memory B cells, naïve CD4+ T cells, activated memory CD4+ T cells, and M1 macrophages. In vitro experiments demonstrated that silencing NCAPD2 suppressed LUAD cell proliferation, migration, invasion, epithelial-mesenchymal transition (EMT), and cell cycle progression.

Conclusions

In summary, NCAPD2 may represent a promising prognostic biomarker and novel therapeutic target for LUAD.

Assessment of Albumin-Incorporating Scores at Hepatocellular Carcinoma Diagnosis Using Machine Learning Techniques: An Evaluation of Prognostic Relevance

Hepatocellular carcinoma (HCC) presents high mortality rates worldwide, with limited evidence on prognostic factors at diagnosis. This study evaluates the utility of common scores incorporating albumin as predictors of mortality at HCC diagnosis using Machine Learning techniques. They are also compared to other scores and variables commonly used. A retrospective cohort study was conducted with 191 patients from Virgen de la Luz Hospital of Cuenca and University Hospital of Guadalajara. Demographic, analytical, and tumor-specific variables were included. Various Machine Learning algorithms were implemented, with eXtreme Gradient Boosting (XGB) as the reference method. In the predictive model developed, the Barcelona Clinic Liver Cancer score was the best predictor of mortality, closely followed by the Platelet-Albumin-Bilirubin and Albumin-Bilirubin scores. Albumin levels alone also showed high relevance. Other scores, such as C-Reactive Protein/albumin and Child-Pugh performed less effectively. XGB proved to be the most accurate method across the metrics analyzed, outperforming other ML algorithms. In conclusion, the Barcelona Clinic Liver Cancer, Platelet-Albumin-Bilirubin and Albumin-Bilirubin scores are highly reliable for assessing survival at HCC diagnosis. The XGB-developed model proved to be the most reliable for this purpose compared to the other proposed methods.

Developing and validating a clinlabomics-based machine-learning model for early detection of retinal detachment in patients with high myopia

BACKGROUND

Retinal detachment (RD) is a vision-threatening disorder of significant severity. Individuals with high myopia (HM) face a 2 to 6 times higher risk of developing RD compared to non-myopes. The timely identification of high myopia-related retinal detachment (HMRD) is crucial for effective treatment and prevention of additional vision impairment. Consequently, our objective was to streamline and validate a machine-learning model based on clinical laboratory omics (clinlabomics) for the early detection of RD in HM patients.

METHODS

We extracted clinlabomics data from the electronic health records for 24,440 HM and 5607 HMRD between 2015 and 2022. Lasso regression analysis assessed fifty-nine variables, excluding collinear variables (variance inflation factor > 10). Four models based on random forest, gradient boosting machine (GBM), generalized linear model, and Deep Learning Model were trained for HMRD diagnosis and employed for internal validation. An external test of the models was done. Three random data sets were further processed to validate the performance of the diagnostic model. The primary outcomes were the area under the receiver operating characteristic curve (AUC) and the area under the precision-recall curve (AUCPR) to diagnose HMRD.

RESULTS

Nine variables were selected by all models. Given the AUC and AUCPR values across the different sets, the GBM model was chosen as the final diagnostic model. The GBM model had an AUC of 0.8550 (95%CI = 0.8322-0.8967) and an AUCPR of 0.5584 (95%CI = 0.5250-0.5879) in the training set. The AUC and AUCPR in the internal validation were 0.8405 (95%CI = 0.8060-0.8966) and 0.5355 (95%CI = 0.4988-0.5732). During the external test evaluation, it reached an AUC of 0.7579 (95%CI = 0.7340-0.7840) and an AUCPR of 0.5587 (95%CI = 0.5345-0.5880). A similar discriminative capacity was observed in the three random data sets. The GBM model was well-calibrated across all the sets. The GBM-RD model was implemented into a web application that provides risk prediction for HM individuals.

CONCLUSION

GBM algorithms based on nine features successfully predicted the diagnosis of RD in patients with HM, which will help ophthalmologists to establish a preliminary diagnosis and to improve diagnostic accuracy in the clinic.

An Ensemble Framework to Forest Optimization Based Reduct Searching

Essentially, the solution to an attribute reduction problem can be viewed as a reduct searching process. Currently, among various searching strategies, meta-heuristic searching has received extensive attention. As a new emerging meta-heuristic approach, the forest optimization algorithm (FOA) is introduced to the problem solving of attribute reduction in this study. To further improve the classification performance of selected attributes in reduct, an ensemble framework is also developed: firstly, multiple reducts are obtained by FOA and data perturbation, and the structure of those multiple reducts is symmetrical, which indicates that no order exists among those reducts; secondly, multiple reducts are used to execute voting classification over testing samples. Finally, comprehensive experiments on over 20 UCI datasets clearly validated the effectiveness of our framework: it is not only beneficial to output reducts with superior classification accuracies and classification stabilities but also suitable for data pre-processing with noise. This improvement work we have performed makes the FOA obtain better benefits in the data processing of life, health, medical and other fields.

The diagnostic accuracy of artificial intelligence in thoracic diseases: A protocol for systematic review and meta-analysis

INTRODUCTION

Thoracic diseases include a variety of common human primary malignant tumors, among which lung cancer and esophageal cancer are among the top 10 in cancer incidence and mortality. Early diagnosis is an important part of cancer treatment, so artificial intelligence (AI) systems have been developed for the accurate and automated detection and diagnosis of thoracic tumors. However, the complicated AI structure and image processing made the diagnosis result of AI-based system unstable. The purpose of this study is to systematically review published evidence to explore the accuracy of AI systems in diagnosing thoracic cancers.

METHODS AND ANALYSIS

We will conduct a systematic review and meta-analysis of the diagnostic accuracy of AI systems for the prediction of thoracic diseases. The primary objective is to assess the diagnostic accuracy of thoracic cancers, including assessing potential biases and calculating combined estimates of sensitivity, specificity, and area under the receiver operating characteristic curve (AUC). The secondary objective is to evaluate the factors associated with different models, classifiers, and radiomics information. We will search databases such as PubMed/MEDLINE, Embase (via OVID), and the Cochrane Library. Two reviewers will independently screen titles and abstracts, perform full article reviews and extract study data. We will report study characteristics and assess methodological quality using the Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS-2) tool. RevMan 5.3 and Meta-disc 1.4 software will be used for data synthesis. If pooling is appropriate, we will produce summary receiver operating characteristic (SROC) curves, summary operating points (pooled sensitivity and specificity), and 95% confidence intervals around the summary operating points. Methodological subgroup and sensitivity analyses will be performed to explore heterogeneity.

PROSPERO REGISTRATION NUMBER

CRD42019135247.

A Computational Approach for the Assessment of Executive Functions in Patients with Obsessive-Compulsive Disorder

Previous studies on obsessive–compulsive disorder (OCD) showed impairments in executive domains, particularly in cognitive inhibition. In this perspective, the use of virtual reality showed huge potential in the assessment of executive functions; however, unfortunately, to date, no study on the assessment of these patients took advantage of the use of virtual environments. One of the main problems faced within assessment protocols is the use of a limited number of variables and tools when tailoring a personalized program. The main aim of this study was to provide a heuristic decision tree for the future development of tailored assessment protocols. To this purpose, we conducted a study that involved 58 participants (29 OCD patients and 29 controls) to collect both classic neuropsychological data and precise data based on a validated protocol in virtual reality for the assessment of executive functions, namely, the VMET (virtual multiple errands test). In order to provide clear indications for working on executive functions with these patients, we carried out a cross-validation based on three learning algorithms and computationally defined two decision trees. We found that, by using three neuropsychological tests and two VMET scores, it was possible to discriminate OCD patients from controls, opening a novel scenario for future assessment protocols based on virtual reality and computational techniques.

Not-so-supervised: A survey of semi-supervised, multi-instance, and transfer learning in medical image analysis

Machine learning (ML) algorithms have made a tremendous impact in the field of medical imaging. While medical imaging datasets have been growing in size, a challenge for supervised ML algorithms that is frequently mentioned is the lack of annotated data. As a result, various methods that can learn with less/other types of supervision, have been proposed. We give an overview of semi-supervised, multiple instance, and transfer learning in medical imaging, both in diagnosis or segmentation tasks. We also discuss connections between these learning scenarios, and opportunities for future research. A dataset with the details of the surveyed papers is available via https://figshare.com/articles/Database_of_surveyed_literature_in_Not-so-supervised_a_survey_of_semi-supervised_multi-instance_and_transfer_learning_in_medical_image_analysis_/7479416.

Computational Psychometrics Using Psychophysiological Measures for the Assessment of Acute Mental Stress

The goal of this study was to provide reliable quantitative analyses of psycho-physiological measures during acute mental stress. Acute, time-limited stressors are used extensively as experimental stimuli in psychophysiological research. In particular, the Stroop Color Word Task and the Arithmetical Task have been widely used in several settings as effective mental stressors. We collected psychophysiological data on blood volume pulse, thoracic respiration, and skin conductance from 60 participants at rest and during stressful situations. Subsequently, we used statistical univariate tests and multivariate computational approaches to conduct comprehensive studies on the discriminative properties of each condition in relation to psychophysiological correlates. The results showed evidence of a greater discrimination capability of the Arithmetical Task compared to the Stroop test. The best predictors were the short time Heart Rate Variability (HRV) indices, in particular, the Respiratory Sinus Arrhythmia index, which in turn could be predicted by other HRV and respiratory indices in a hierarchical, multi-level regression analysis. Thus, computational psychometrics analyses proved to be an effective tool for studying such complex variables. They could represent the first step in developing complex platforms for the automatic detection of mental stress, which could improve the treatment.

Progressive Semisupervised Learning of Multiple Classifiers

Semisupervised learning methods are often adopted to handle datasets with very small number of labeled samples. However, conventional semisupervised ensemble learning approaches have two limitations: 1) most of them cannot obtain satisfactory results on high dimensional datasets with limited labels and 2) they usually do not consider how to use an optimization process to enlarge the training set. In this paper, we propose the progressive semisupervised ensemble learning approach (PSEMISEL) to address the above limitations and handle datasets with very small number of labeled samples. When compared with traditional semisupervised ensemble learning approaches, PSEMISEL is characterized by two properties: 1) it adopts the random subspace technique to investigate the structure of the dataset in the subspaces and 2) a progressive training set generation process and a self evolutionary sample selection process are proposed to enlarge the training set. We also use a set of nonparametric tests to compare different semisupervised ensemble learning methods over multiple datasets. The experimental results on 18 real-world datasets from the University of California, Irvine machine learning repository show that PSEMISEL works well on most of the real-world datasets, and outperforms other state-of-the-art approaches on 10 out of 18 datasets.