Improved NSGA-II algorithms for multi-objective biomarker discovery.

MOTIVATION: In modern translational research, the development of biomarkers heavily relies on use of omics technologies, but implementations with basic data mining algorithms frequently lead to false positives. Non-dominated Sorting Genetic Algorithm II (NSGA2) is an extremely effective algorithm for biomarker discovery but has been rarely evaluated against large-scale datasets. The exploration of the feature search space is the key to NSGA2 success but in specific cases NSGA2 expresses a shallow exploration of the space of possible feature combinations, possibly leading to models with low predictive performances. RESULTS: We propose two improved NSGA2 algorithms for finding subsets of biomarkers exhibiting different trade-offs between accuracy and feature number. The performances are investigated on gene expression data of breast cancer patients. The results are compared with NSGA2 and LASSO. The benchmarking dataset includes internal and external validation sets. The results show that the proposed algorithms generate a better approximation of the optimal trade-offs between accuracy and set size. Moreover, validation and test accuracies are better than those provided by NSGA2 and LASSO. Remarkably, the GA-based methods provide biomarkers that achieve a very high prediction accuracy (>80%) with a small number of features (<10), representing a valid alternative to known biomarker models, such as Pam50 and MammaPrint. AVAILABILITY AND IMPLEMENTATION: The software is publicly available on GitHub at github.com/UEFBiomedicalInformaticsLab/BIODAI/tree/main/MOO. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Risk Prediction Models for Depression in Community-Dwelling Older Adults.

OBJECTIVE: To develop streamlined Risk Prediction Models (Manto RPMs) for late-life depression. DESIGN: Prospective study. SETTING: The Survey of Health, Ageing and Retirement in Europe (SHARE) study. PARTICIPANTS: Participants were community residing adults aged 55 years or older. MEASUREMENTS: The outcome was presence of depression at a 2-year follow up evaluation. Risk factors were identified after a literature review of longitudinal studies. Separate RPMs were developed in the 29,116 participants who were not depressed at baseline and in the combined sample of 39,439 of non-depressed and depressed subjects. Models derived from the combined sample were used to develop a web-based risk calculator. RESULTS: The authors identified 129 predictors of late-life depression after reviewing 227 studies. In non-depressed participants at baseline, the RPMs based on regression and Least Absolute Shrinkage and Selection Operator (LASSO) penalty (34 and 58 predictors, respectively) and the RPM based on Artificial Neural Networks (124 predictors) had a similar performance (AUC: 0.730-0.743). In the combined depressed and non-depressed participants at baseline, the RPM based on neural networks (35 predictors; AUC: 0.807; 95% CI: 0.80-0.82) and the model based on linear regression and LASSO penalty (32 predictors; AUC: 0.81; 95% CI: 0.79-0.82) had satisfactory accuracy. CONCLUSIONS: The Manto RPMs can identify community-dwelling older individuals at risk for developing depression over 2 years. A web-based calculator based on the streamlined Manto model is freely available at https://manto.unife.it/ for use by individuals, clinicians, and policy makers and may be used to target prevention interventions at the individual and the population levels.

Nextcast: A software suite to analyse and model toxicogenomics data.

The recent advancements in toxicogenomics have led to the availability of large omics data sets, representing the starting point for studying the exposure mechanism of action and identifying candidate biomarkers for toxicity prediction. The current lack of standard methods in data generation and analysis hampers the full exploitation of toxicogenomics-based evidence in regulatory risk assessment. Moreover, the pipelines for the preprocessing and downstream analyses of toxicogenomic data sets can be quite challenging to implement. During the years, we have developed a number of software packages to address specific questions related to multiple steps of toxicogenomics data analysis and modelling. In this review we present the Nextcast software collection and discuss how its individual tools can be combined into efficient pipelines to answer specific biological questions. Nextcast components are of great support to the scientific community for analysing and interpreting large data sets for the toxicity evaluation of compounds in an unbiased, straightforward, and reliable manner. The Nextcast software suite is available at: ( https://github.com/fhaive/nextcast).

Computationally prioritized drugs inhibit SARS-CoV-2 infection and syncytia formation.

The pharmacological arsenal against the COVID-19 pandemic is largely based on generic anti-inflammatory strategies or poorly scalable solutions. Moreover, as the ongoing vaccination campaign is rolling slower than wished, affordable and effective therapeutics are needed. To this end, there is increasing attention toward computational methods for drug repositioning and de novo drug design. Here, multiple data-driven computational approaches are systematically integrated to perform a virtual screening and prioritize candidate drugs for the treatment of COVID-19. From the list of prioritized drugs, a subset of representative candidates to test in human cells is selected. Two compounds, 7-hydroxystaurosporine and bafetinib, show synergistic antiviral effects in vitro and strongly inhibit viral-induced syncytia formation. Moreover, since existing drug repositioning methods provide limited usable information for de novo drug design, the relevant chemical substructures of the identified drugs are extracted to provide a chemical vocabulary that may help to design new effective drugs.

Supervised Methods for Biomarker Detection from Microarray Experiments.

Biomarkers are valuable indicators of the state of a biological system. Microarray technology has been extensively used to identify biomarkers and build computational predictive models for disease prognosis, drug sensitivity and toxicity evaluations. Activation biomarkers can be used to understand the underlying signaling cascades, mechanisms of action and biological cross talk. Biomarker detection from microarray data requires several considerations both from the biological and computational points of view. In this chapter, we describe the main methodology used in biomarkers discovery and predictive modeling and we address some of the related challenges. Moreover, we discuss biomarker validation and give some insights into multiomics strategies for biomarker detection.

Unsupervised Algorithms for Microarray Sample Stratification.

The amount of data made available by microarrays gives researchers the opportunity to delve into the complexity of biological systems. However, the noisy and extremely high-dimensional nature of this kind of data poses significant challenges. Microarrays allow for the parallel measurement of thousands of molecular objects spanning different layers of interactions. In order to be able to discover hidden patterns, the most disparate analytical techniques have been proposed. Here, we describe the basic methodologies to approach the analysis of microarray datasets that focus on the task of (sub)group discovery.

Network Analysis of Microarray Data.

DNA microarrays are widely used to investigate gene expression. Even though the classical analysis of microarray data is based on the study of differentially expressed genes, it is well known that genes do not act individually. Network analysis can be applied to study association patterns of the genes in a biological system. Moreover, it finds wide application in differential coexpression analysis between different systems. Network based coexpression studies have for example been used in (complex) disease gene prioritization, disease subtyping, and patient stratification.In this chapter we provide an overview of the methods and tools used to create networks from microarray data and describe multiple methods on how to analyze a single network or a group of networks. The described methods range from topological metrics, functional group identification to data integration strategies, topological pathway analysis as well as graphical models.

Identifying gene expression-based biomarkers in online learning environments.

Motivation: Gene expression-based classifiers are often developed using historical data by training a model on a small set of patients and a large set of features. Models trained in such a way can be afterwards applied for predicting the output for new unseen patient data. However, very often the accuracy of these models starts to decrease as soon as new data is fed into the trained model. This problem, known as concept drift, complicates the task of learning efficient biomarkers from data and requires special approaches, different from commonly used data mining techniques. Results: Here, we propose an online ensemble learning method to continually validate and adjust gene expression-based biomarker panels over increasing volume of data. We also propose a computational solution to the problem of feature drift where gene expression signatures used to train the classifier become less relevant over time. A benchmark study was conducted to classify the breast tumors into known subtypes by using a large-scale transcriptomic dataset (∼3500 patients), which was obtained by combining two datasets: SCAN-B and TCGA-BRCA. Remarkably, the proposed strategy improves the classification performances of gold-standard biomarker panels (e.g. PAM50, OncotypeDX and Endopredict) by adding features that are clinically relevant. Moreover, test results show that newly discovered biomarker models can retain a high classification accuracy rate when changing the source generating the gene expression profiles. Availability and implementation: github.com/UEFBiomedicalInformaticsLab/OnlineLearningBD. Supplementary information: Supplementary data are available at Bioinformatics Advances online.

Transcriptomics in Toxicogenomics, Part II: Preprocessing and Differential Expression Analysis for High Quality Data.

Preprocessing of transcriptomics data plays a pivotal role in the development of toxicogenomics-driven tools for chemical toxicity assessment. The generation and exploitation of large volumes of molecular profiles, following an appropriate experimental design, allows the employment of toxicogenomics (TGx) approaches for a thorough characterisation of the mechanism of action (MOA) of different compounds. To date, a plethora of data preprocessing methodologies have been suggested. However, in most cases, building the optimal analytical workflow is not straightforward. A careful selection of the right tools must be carried out, since it will affect the downstream analyses and modelling approaches. Transcriptomics data preprocessing spans across multiple steps such as quality check, filtering, normalization, batch effect detection and correction. Currently, there is a lack of standard guidelines for data preprocessing in the TGx field. Defining the optimal tools and procedures to be employed in the transcriptomics data preprocessing will lead to the generation of homogeneous and unbiased data, allowing the development of more reliable, robust and accurate predictive models. In this review, we outline methods for the preprocessing of three main transcriptomic technologies including microarray, bulk RNA-Sequencing (RNA-Seq), and single cell RNA-Sequencing (scRNA-Seq). Moreover, we discuss the most common methods for the identification of differentially expressed genes and to perform a functional enrichment analysis. This review is the second part of a three-article series on Transcriptomics in Toxicogenomics.

Transcriptomics in Toxicogenomics, Part I: Experimental Design, Technologies, Publicly Available Data, and Regulatory Aspects.

The starting point of successful hazard assessment is the generation of unbiased and trustworthy data. Conventional toxicity testing deals with extensive observations of phenotypic endpoints in vivo and complementing in vitro models. The increasing development of novel materials and chemical compounds dictates the need for a better understanding of the molecular changes occurring in exposed biological systems. Transcriptomics enables the exploration of organisms' responses to environmental, chemical, and physical agents by observing the molecular alterations in more detail. Toxicogenomics integrates classical toxicology with omics assays, thus allowing the characterization of the mechanism of action (MOA) of chemical compounds, novel small molecules, and engineered nanomaterials (ENMs). Lack of standardization in data generation and analysis currently hampers the full exploitation of toxicogenomics-based evidence in risk assessment. To fill this gap, TGx methods need to take into account appropriate experimental design and possible pitfalls in the transcriptomic analyses as well as data generation and sharing that adhere to the FAIR (Findable, Accessible, Interoperable, and Reusable) principles. In this review, we summarize the recent advancements in the design and analysis of DNA microarray, RNA sequencing (RNA-Seq), and single-cell RNA-Seq (scRNA-Seq) data. We provide guidelines on exposure time, dose and complex endpoint selection, sample quality considerations and sample randomization. Furthermore, we summarize publicly available data resources and highlight applications of TGx data to understand and predict chemical toxicity potential. Additionally, we discuss the efforts to implement TGx into regulatory decision making to promote alternative methods for risk assessment and to support the 3R (reduction, refinement, and replacement) concept. This review is the first part of a three-article series on Transcriptomics in Toxicogenomics. These initial considerations on Experimental Design, Technologies, Publicly Available Data, Regulatory Aspects, are the starting point for further rigorous and reliable data preprocessing and modeling, described in the second and third part of the review series.

Transcriptomics in Toxicogenomics, Part III: Data Modelling for Risk Assessment.

Transcriptomics data are relevant to address a number of challenges in Toxicogenomics (TGx). After careful planning of exposure conditions and data preprocessing, the TGx data can be used in predictive toxicology, where more advanced modelling techniques are applied. The large volume of molecular profiles produced by omics-based technologies allows the development and application of artificial intelligence (AI) methods in TGx. Indeed, the publicly available omics datasets are constantly increasing together with a plethora of different methods that are made available to facilitate their analysis, interpretation and the generation of accurate and stable predictive models. In this review, we present the state-of-the-art of data modelling applied to transcriptomics data in TGx. We show how the benchmark dose (BMD) analysis can be applied to TGx data. We review read across and adverse outcome pathways (AOP) modelling methodologies. We discuss how network-based approaches can be successfully employed to clarify the mechanism of action (MOA) or specific biomarkers of exposure. We also describe the main AI methodologies applied to TGx data to create predictive classification and regression models and we address current challenges. Finally, we present a short description of deep learning (DL) and data integration methodologies applied in these contexts. Modelling of TGx data represents a valuable tool for more accurate chemical safety assessment. This review is the third part of a three-article series on Transcriptomics in Toxicogenomics.

Development of a clinical prediction model for the onset of functional decline in people aged 65-75 years: pooled analysis of four European cohort studies.

BACKGROUND: Identifying those people at increased risk of early functional decline in activities of daily living (ADL) is essential for initiating preventive interventions. The aim of this study is to develop and validate a clinical prediction model for onset of functional decline in ADL in three years of follow-up in older people of 65-75 years old. METHODS: Four population-based cohort studies were pooled for the analysis: ActiFE-ULM (Germany), ELSA (United Kingdom), InCHIANTI (Italy), LASA (Netherlands). Included participants were 65-75 years old at baseline and reported no limitations in functional ability in ADL at baseline. Functional decline was assessed with two items on basic ADL and three items on instrumental ADL. Participants who reported at least some limitations at three-year follow-up on any of the five items were classified as experiencing functional decline. Multiple logistic regression analysis was used to develop a prediction model, with subsequent bootstrapping for optimism-correction. We applied internal-external cross-validation by alternating the data from the four cohort studies to assess the discrimination and calibration across the cohorts. RESULTS: Two thousand five hundred sixty community-dwelling people were included in the analyses (mean age 69.7 ± 3.0 years old, 47.4% female) of whom 572 (22.3%) reported functional decline at three-year follow-up. The final prediction model included 10 out of 22 predictors: age, handgrip strength, gait speed, five-repeated chair stands time (non-linear association), body mass index, cardiovascular disease, diabetes, chronic obstructive pulmonary disease, arthritis, and depressive symptoms. The optimism-corrected model showed good discrimination with a C statistic of 0.72. The calibration intercept was 0.06 and the calibration slope was 1.05. Internal-external cross-validation showed consistent performance of the model across the four cohorts. CONCLUSIONS: Based on pooled cohort data analyses we were able to show that the onset of functional decline in ADL in three years in older people aged 65-75 years can be predicted by specific physical performance measures, age, body mass index, presence of depressive symptoms, and chronic conditions. The prediction model showed good discrimination and calibration, which remained stable across the four cohorts, supporting external validity of our findings.

Risk Prediction Model for Late Life Depression: Development and Validation on Three Large European Datasets.

Assessing the risk to develop a specific disease is the first step towards prevention, both at individual and population levels. The development and validation of risk prediction models (RPMs) is the norm within different fields of medicine but still underused in psychiatry, despite the global impact of mental disorders. In particular, there is a lack of RPMs to assess the risk of developing depression, the first worldwide cause of disability and harbinger of functional decline in old age. We present the depression risk assessment tool DRAT-up, the first prospective RPM to identify late-life depression among community-dwelling subjects aged 60-75. The development of DRAT-up was based on appraisal of relevant literature, extraction of robust risk estimates, and integration into model parameters. A unique feature is the ability to estimate risk even in the presence of missing values. To assess the properties of DRAT-up, a validation study was conducted on three European cohorts, namely, the English Longitudinal Study of Ageing, the Invecchiare nel Chianti, and the Irish Longitudinal Study on Ageing, with 20 206, 1359, and 3124 eligible samples, respectively. The model yielded accurate risk estimation in the three datasets from a small number of predictors. The Brier scores were 0.054, 0.133, and 0.041, respectively, while the values of area under the curve (AUC) were 0.761, 0.736, and 0.768, respectively. Sensitivity analyses suggest robustness to missing values: setting any individual feature to unknown caused the Brier scores to increase by 0.004 and the AUCs to decrease by 0.045 in the worst cases. DRAT-up can be readily used for clinical purposes and to aid policy-making in the field of mental health.

Predicting Trajectories of Functional Decline in 60- to 70-Year-Old People.

BACKGROUND: Early identification of people at risk of functional decline is essential for delivering targeted preventive interventions. OBJECTIVE: The aim of this study is to identify and predict trajectories of functional decline over 9 years in males and females aged 60-70 years. METHODS: We included 403 community-dwelling participants from the InCHIANTI study and 395 from the LASA study aged 60-70 years at baseline, of whom the majority reported no functional decline at baseline (median 0, interquartile range 0-1). Participants were included if they reported data on ≥2 measurements of functional ability during a 9-year follow-up. Functional ability was scored with 6 self-reported items on activities of daily living. We performed latent class growth analysis to identify trajectories of functional decline and applied multinomial regression models to develop prediction models of identified trajectories. Analyses were stratified for sex. RESULTS: Three distinct trajectories were identified: no/little decline (219 males, 241 females), intermediate decline (114 males, 158 females), and severe decline (36 males, 30 females). Higher gait speed showed decreased risk of functional limitations in males (intermediate limitations, odds ratio [OR] 0.74, 95% CI 0.57-0.97; severe limitations, OR 0.42, 95% CI 0.26-0.66). The final model in males further included the predictors fear of falling and alcohol intake (no/little decline, area under the receiver operating curve [AUC] 0.68, 95% CI 0.62-0.73; intermediate decline, AUC 0.63, 95% CI 0.56-0.69; severe decline, AUC 0.79, 95% CI 0.71-0.87). In females, higher gait speed showed a decreased risk of intermediate limitations (OR 0.51, 95% CI 0.38-0.68) and severe limitations (OR 0.18, 95% CI 0.07-0.44). Other predictors in females were age, living alone, economic satisfaction, balance, physical activity, BMI, and cardiovascular disease (no/little decline, AUC 0.80, 95% CI 0.75-0.85; intermediate decline, AUC 0.74, 95% CI 0.69-0.79; severe decline, AUC 0.95, 95% CI 0.91-0.99). CONCLUSION: Already in people aged 60-70 years, 3 distinct trajectories of functional decline were identified in these cohorts over a 9-year follow-up. Predictors of trajectories differed between males and females, except for gait speed. Identification of people at risk is the basis for targeting interventions.

Predictive Performance of a Fall Risk Assessment Tool for Community-Dwelling Older People (FRAT-up) in 4 European Cohorts.

BACKGROUND AND OBJECTIVE: The fall risk assessment tool (FRAT-up) is a tool for predicting falls in community-dwelling older people based on a meta-analysis of fall risk factors. Based on the fall risk factor profile, this tool calculates the individual risk of falling over the next year. The objective of this study is to evaluate the performance of FRAT-up in predicting future falls in multiple cohorts. METHODS: Information about fall risk factors in 4 European cohorts of older people [Activity and Function in the Elderly (ActiFE), Germany; English Longitudinal Study of Aging (ELSA), England; Invecchiare nel Chianti (InCHIANTI), Italy; Irish Longitudinal Study on Aging (TILDA), Ireland] was used to calculate the FRAT-up risk score in individual participants. Information about falls that occurred after the assessment of the risk factors was collected from subsequent longitudinal follow-ups. We compared the performance of FRAT-up against those of other prediction models specifically fitted in each cohort by calculation of the area under the receiver operating characteristic curve (AUC). RESULTS: The AUC attained by FRAT-up is 0.562 [95% confidence interval (CI) 0.530-0.594] for ActiFE, 0.699 (95% CI 0.680-0.718) for ELSA, 0.636 (95% CI 0.594-0.681) for InCHIANTI, and 0.685 (95% CI 0.660-0.709) for TILDA. Mean FRAT-up AUC as estimated from meta-analysis is 0.646 (95% CI 0.584-0.708), with substantial heterogeneity between studies. In each cohort, FRAT-up discriminant ability is surpassed, at most, by the cohort-specific risk model fitted on that same cohort. CONCLUSIONS: We conclude that FRAT-up is a valid approach to estimate risk of falls in populations of community-dwelling older people. However, further studies should be performed to better understand the reasons for the observed heterogeneity across studies and to refine a tool that performs homogeneously with higher accuracy measures across different populations.

FRAT-up, a Web-based fall-risk assessment tool for elderly people living in the community.

BACKGROUND: About 30% of people over 65 are subject to at least one unintentional fall a year. Fall prevention protocols and interventions can decrease the number of falls. To be effective, a prevention strategy requires a prior step to evaluate the fall risk of the subjects. Despite extensive research, existing assessment tools for fall risk have been insufficient for predicting falls. OBJECTIVE: The goal of this study is to present a novel web-based fall-risk assessment tool (FRAT-up) and to evaluate its accuracy in predicting falls, within a context of community-dwelling persons aged 65 and up. METHODS: FRAT-up is based on the assumption that a subject's fall risk is given by the contribution of their exposure to each of the known fall-risk factors. Many scientific studies have investigated the relationship between falls and risk factors. The majority of these studies adopted statistical approaches, usually providing quantitative information such as odds ratios. FRAT-up exploits these numerical results to compute how each single factor contributes to the overall fall risk. FRAT-up is based on a formal ontology that enlists a number of known risk factors, together with quantitative findings in terms of odds ratios. From such information, an automatic algorithm generates a rule-based probabilistic logic program, that is, a set of rules for each risk factor. The rule-based program takes the health profile of the subject (in terms of exposure to the risk factors) and computes the fall risk. A Web-based interface allows users to input health profiles and to visualize the risk assessment for the given subject. FRAT-up has been evaluated on the InCHIANTI Study dataset, a representative population-based study of older persons living in the Chianti area (Tuscany, Italy). We compared reported falls with predicted ones and computed performance indicators. RESULTS: The obtained area under curve of the receiver operating characteristic was 0.642 (95% CI 0.614-0.669), while the Brier score was 0.174. The Hosmer-Lemeshow test indicated statistical significance of miscalibration. CONCLUSIONS: FRAT-up is a web-based tool for evaluating the fall risk of people aged 65 or up living in the community. Validation results of fall risks computed by FRAT-up show that its performance is comparable to externally validated state-of-the-art tools. A prototype is freely available through a web-based interface. TRIAL REGISTRATION: ClinicalTrials.gov NCT01331512 (The InChianti Follow-Up Study); http://clinicaltrials.gov/show/NCT01331512 (Archived by WebCite at http://www.webcitation.org/6UDrrRuaR).