A comparison of methods for interpreting random forest models of genetic association in the presence of non-additive interactions

Comparing statistical learning methods for complex trait prediction from gene expression

Accurate prediction of complex traits is an important task in quantitative genetics that has become increasingly relevant for personalized medicine. Genotypes have traditionally been used for trait prediction using a variety of methods such as mixed models, Bayesian methods, penalized regressions, dimension reductions, and machine learning methods. Recent studies have shown that gene expression levels can produce higher prediction accuracy than genotypes. However, only a few prediction methods were used in these studies. Thus, a comprehensive assessment of methods is needed to fully evaluate the potential of gene expression as a predictor of complex trait phenotypes. Here, we used data from the Drosophila Genetic Reference Panel (DGRP) to compare the ability of several existing statistical learning methods to predict starvation resistance from gene expression in the two sexes separately. The methods considered differ in assumptions about the distribution of gene effect sizes - ranging from models that assume that every gene affects the trait to more sparse models - and their ability to capture gene-gene interactions. We also used functional annotation (i.e., Gene Ontology (GO)) as an external source of biological information to inform prediction models. The results show that differences in prediction accuracy between methods exist, although they are generally not large. Methods performing variable selection gave higher accuracy in females while methods assuming a more polygenic architecture performed better in males. Incorporating GO annotations further improved prediction accuracy for a few GO terms of biological significance. Biological significance extended to the genes underlying highly predictive GO terms with different genes emerging between sexes. Notably, the Insulin-like Receptor (InR) was prevalent across methods and sexes. Our results confirmed the potential of transcriptomic prediction and highlighted the importance of selecting appropriate methods and strategies in order to achieve accurate predictions.

Protein characteristics substantially influence the propensity of activity cliffs among kinase inhibitors

Activity cliffs (ACs) are pairs of structurally similar molecules with significantly different affinities for a biotarget, posing a challenge in computer-assisted drug discovery. This study focuses on protein kinases, significant therapeutic targets, with some exhibiting ACs while others do not despite numerous inhibitors. The hypothesis that the presence of ACs is dependent on the target protein and its complete structural context is explored. Machine learning models were developed to link protein properties to ACs, revealing specific tripeptide sequences and overall protein properties as critical factors in ACs occurrence. The study highlights the importance of considering the entire protein matrix rather than just the binding site in understanding ACs. This research provides valuable insights for drug discovery and design, paving the way for addressing ACs-related challenges in modern computational approaches.

Artificial Intelligence Modeling to Predict Periprosthetic Infection and Explantation following Implant-Based Reconstruction

BACKGROUND

Despite improvements in prosthesis design and surgical techniques, periprosthetic infection and explantation rates following implant-based reconstruction (IBR) remain relatively high. Artificial intelligence is an extremely powerful predictive tool that involves machine learning (ML) algorithms. We sought to develop, validate, and evaluate the use of ML algorithms to predict complications of IBR.

METHODS

A comprehensive review of patients who underwent IBR from January of 2018 to December of 2019 was conducted. Nine supervised ML algorithms were developed to predict periprosthetic infection and explantation. Patient data were randomly divided into training (80%) and testing (20%) sets.

RESULTS

The authors identified 481 patients (694 reconstructions) with a mean ± SD age of 50.0 ± 11.5 years, mean ± SD body mass index of 26.7 ± 4.8 kg/m 2 , and median follow-up time of 16.1 months (range, 11.9 to 3.2 months). Periprosthetic infection developed in 113 of the reconstructions (16.3%), and explantation was required with 82 (11.8%) of them. ML demonstrated good discriminatory performance in predicting periprosthetic infection and explantation (area under the receiver operating characteristic curve, 0.73 and 0.78, respectively), and identified nine and 12 significant predictors of periprosthetic infection and explantation, respectively.

CONCLUSIONS

ML algorithms trained using readily available perioperative clinical data accurately predict periprosthetic infection and explantation following IBR. The authors' findings support incorporating ML models into perioperative assessment of patients undergoing IBR to provide data-driven, patient-specific risk assessment to aid individualized patient counseling, shared decision-making, and presurgical optimization.

Discovering SNP-disease relationships in genome-wide SNP data using an improved harmony search based on SNP locus and genetic inheritance patterns

Advances in high-throughput sequencing technologies have made it possible to access millions of measurements from thousands of people. Single nucleotide polymorphisms (SNPs), the most common type of mutation in the human genome, have been shown to play a significant role in the development of complex and multifactorial diseases. However, studying the synergistic interactions between different SNPs in explaining multifactorial diseases is challenging due to the high dimensionality of the data and methodological complexities. Existing solutions often use a multi-objective approach based on metaheuristic optimization algorithms such as harmony search. However, previous studies have shown that using a multi-objective approach is not sufficient to address complex disease models with no or low marginal effect. In this research, we introduce a locus-driven harmony search (LDHS), an improved harmony search algorithm that focuses on using SNP locus information and genetic inheritance patterns to initialize harmony memories. The proposed method integrates biological knowledge to improve harmony memory initialization by adding SNP combinations that are likely candidates for interaction and disease causation. Using a SNP grouping process, LDHS generates harmonies that include SNPs with a higher potential for interaction, resulting in greater power in detecting disease-causing SNP combinations. The performance of the proposed algorithm was evaluated on 200 synthesized datasets for disease models with and without marginal effect. The results show significant improvement in the power of the algorithm to find disease-related SNP sets while decreasing computational cost compared to state-of-the-art algorithms. The proposed algorithm also demonstrated notable performance on real breast cancer data, showing that integrating prior knowledge can significantly improve the process of detecting disease-related SNPs in both real and synthesized data.

Automated quantitative trait locus analysis (AutoQTL)

BACKGROUND

Quantitative Trait Locus (QTL) analysis and Genome-Wide Association Studies (GWAS) have the power to identify variants that capture significant levels of phenotypic variance in complex traits. However, effort and time are required to select the best methods and optimize parameters and pre-processing steps. Although machine learning approaches have been shown to greatly assist in optimization and data processing, applying them to QTL analysis and GWAS is challenging due to the complexity of large, heterogenous datasets. Here, we describe proof-of-concept for an automated machine learning approach, AutoQTL, with the ability to automate many complicated decisions related to analysis of complex traits and generate solutions to describe relationships that exist in genetic data.

RESULTS

Using a publicly available dataset of 18 putative QTL from a large-scale GWAS of body mass index in the laboratory rat, Rattus norvegicus, AutoQTL captures the phenotypic variance explained under a standard additive model. AutoQTL also detects evidence of non-additive effects including deviations from additivity and 2-way epistatic interactions in simulated data via multiple optimal solutions. Additionally, feature importance metrics provide different insights into the inheritance models and predictive power of multiple GWAS-derived putative QTL.

CONCLUSIONS

This proof-of-concept illustrates that automated machine learning techniques can complement standard approaches and have the potential to detect both additive and non-additive effects via various optimal solutions and feature importance metrics. In the future, we aim to expand AutoQTL to accommodate omics-level datasets with intelligent feature selection and feature engineering strategies.

Toward characterizing cardiovascular fitness using machine learning based on unobtrusive data

Cardiopulmonary exercise testing (CPET) is a non-invasive approach to measure the maximum oxygen uptake ([Formula: see text]), which is an index to assess cardiovascular fitness (CF). However, CPET is not available to all populations and cannot be obtained continuously. Thus, wearable sensors are associated with machine learning (ML) algorithms to investigate CF. Therefore, this study aimed to predict CF by using ML algorithms using data obtained by wearable technologies. For this purpose, 43 volunteers with different levels of aerobic power, who wore a wearable device to collect unobtrusive data for 7 days, were evaluated by CPET. Eleven inputs (sex, age, weight, height, and body mass index, breathing rate, minute ventilation, total hip acceleration, walking cadence, heart rate, and tidal volume) were used to predict the [Formula: see text] by support vector regression (SVR). Afterward, the SHapley Additive exPlanations (SHAP) method was used to explain their results. SVR was able to predict the CF, and the SHAP method showed that the inputs related to hemodynamic and anthropometric domains were the most important ones to predict the CF. Therefore, we conclude that the cardiovascular fitness can be predicted by wearable technologies associated with machine learning during unsupervised activities of daily living.

Automated quantitative trait locus analysis (AutoQTL)

Background

Quantitative Trait Locus (QTL) analysis and Genome-Wide Association Studies (GWAS) have the power to identify variants that capture significant levels of phenotypic variance in complex traits. However, effort and time are required to select the best methods and optimize parameters and pre-processing steps. Although machine learning approaches have been shown to greatly assist in optimization and data processing, applying them to QTL analysis and GWAS is challenging due to the complexity of large, heterogenous datasets. Here, we describe proof-of-concept for an automated machine learning approach, AutoQTL, with the ability to automate many complex decisions related to analysis of complex traits and generate diverse solutions to describe relationships that exist in genetic data.

Results

Using a dataset of 18 putative QTL from a large-scale GWAS of body mass index in the laboratory rat, Rattus norvegicus , AutoQTL captures the phenotypic variance explained under a standard additive model while also providing evidence of non-additive effects including deviations from additivity and 2-way epistatic interactions from simulated data via multiple optimal solutions. Additionally, feature importance metrics provide different insights into the inheritance models and predictive power of multiple GWAS-derived putative QTL.

Conclusions

This proof-of-concept illustrates that automated machine learning techniques can be applied to genetic data and has the potential to detect both additive and non-additive effects via various optimal solutions and feature importance metrics. In the future, we aim to expand AutoQTL to accommodate omics-level datasets with intelligent feature selection strategies.

A Surgeon's Guide to Artificial Intelligence-Driven Predictive Models

Artificial intelligence (AI) focuses on processing and interpreting complex information as well as identifying relationships and patterns among complex data. Artificial intelligence- and machine learning (ML)-driven predictions have shown promising potential in influencing real-time decisions and improving surgical outcomes by facilitating screening, diagnosis, risk assessment, preoperative planning, and shared decision-making. Fundamental understanding of the algorithms, as well as their development and interpretation, is essential for the evolution of AI in surgery. In this article, we provide surgeons with a fundamental understanding of AI-driven predictive models through an overview of common ML and deep learning algorithms, model development, performance metrics and interpretation. This would serve as a basis for understanding ML-based research, while fostering new ideas and innovations for furthering the reach of this emerging discipline.

The promise of automated machine learning for the genetic analysis of complex traits

The genetic analysis of complex traits has been dominated by parametric statistical methods due to their theoretical properties, ease of use, computational efficiency, and intuitive interpretation. However, there are likely to be patterns arising from complex genetic architectures which are more easily detected and modeled using machine learning methods. Unfortunately, selecting the right machine learning algorithm and tuning its hyperparameters can be daunting for experts and non-experts alike. The goal of automated machine learning (AutoML) is to let a computer algorithm identify the right algorithms and hyperparameters thus taking the guesswork out of the optimization process. We review the promises and challenges of AutoML for the genetic analysis of complex traits and give an overview of several approaches and some example applications to omics data. It is our hope that this review will motivate studies to develop and evaluate novel AutoML methods and software in the genetics and genomics space. The promise of AutoML is to enable anyone, regardless of training or expertise, to apply machine learning as part of their genetic analysis strategy.

What makes a good prediction? Feature importance and beginning to open the black box of machine learning in genetics

Genetic data have become increasingly complex within the past decade, leading researchers to pursue increasingly complex questions, such as those involving epistatic interactions and protein prediction. Traditional methods are ill-suited to answer these questions, but machine learning (ML) techniques offer an alternative solution. ML algorithms are commonly used in genetics to predict or classify subjects, but some methods evaluate which features (variables) are responsible for creating a good prediction; this is called feature importance. This is critical in genetics, as researchers are often interested in which features (e.g., SNP genotype or environmental exposure) are responsible for a good prediction. This allows for the deeper analysis beyond simple prediction, including the determination of risk factors associated with a given phenotype. Feature importance further permits the researcher to peer inside the black box of many ML algorithms to see how they work and which features are critical in informing a good prediction. This review focuses on ML methods that provide feature importance metrics for the analysis of genetic data. Five major categories of ML algorithms: k nearest neighbors, artificial neural networks, deep learning, support vector machines, and random forests are described. The review ends with a discussion of how to choose the best machine for a data set. This review will be particularly useful for genetic researchers looking to use ML methods to answer questions beyond basic prediction and classification.

Machine learning based disease prediction from genotype data

Using results from genome-wide association studies for understanding complex traits is a current challenge. Here we review how genotype data can be used with different machine learning (ML) methods to predict phenotype occurrence and severity from genotype data. We discuss common feature encoding schemes and how studies handle the often small number of samples compared to the huge number of variants. We compare which ML methods are being applied, including recent results using deep neural networks. Further, we review the application of methods for feature explanation and interpretation.