In this contribution we describe an approach to evolve composite covariance functions for Gaussian processes using genetic programming. A critical aspect of Gaussian processes and similar kernel-based models such as SVM is, that the covariance function should be adapted to the modeled data. Frequently, the squared expo…
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48 results for “genetic covariates”
EB-VAE combines tumor growth and dropout data for personalized treatment response modeling.
problem Challenges in integrating longitudinal tumor measurements, dropout information, and genetic covariates.
method Extended EB-VAE framework to jointly model longitudinal and time-to-event data, incorporating dropout hazard and genetic covariates.
result Hybrid decoder formulation yields consistent treatment-effect parameters and prior predictive performance comparable to neural decoder.
New hierarchical model improves on standard practice for high-dimensional data.
problem Poor statistical performance in high-dimensional hierarchical models.
method Model effects as exchangeable across covariates and correlated across datasets.
result Empirical Bayes estimator outperforms classic approach in high-dimensional settings.
Identifying Outliers using Influence Function of Multiple Kernel Canonical Correlation Analysisstat.ML
Imaging genetic research has essentially focused on discovering unique and co-association effects, but typically ignoring to identify outliers or atypical objects in genetic as well as non-genetics variables. Identifying significant outliers is an essential and challenging issue for imaging genetics and multiple source…
Bayesian method selects important covariates in modal regression.
problem Bayesian modal regression with heavy-tailed responses.
method Expectation-maximization algorithm for parameter estimation; test statistic for variable selection.
result Efficacy of the proposed method in identifying important covariates.
Big data applications, such as medical imaging and genetics, typically generate datasets that consist of few observations n on many more variables p, a scenario that we denote as p>>n. Traditional data processing methods are often insufficient for extracting information out of big data. This calls for the development o…
Associating genetic markers with a multidimensional phenotype is an important yet challenging problem. In this work, we establish the equivalence between two popular methods: kernel-machine regression (KMR), and kernel distance covariance (KDC). KMR is a semiparametric regression frameworks that models the covariate ef…
The central aim in this paper is to address variable selection questions in nonlinear and nonparametric regression. Motivated by statistical genetics, where nonlinear interactions are of particular interest, we introduce a novel and interpretable way to summarize the relative importance of predictor variables. Methodol…
Develops a GP framework for age and year-specific mortality surfaces.
problem Learning the covariance structure of age and year-specific mortality surfaces.
method Genetic programming algorithm to search for the most expressive GP kernel.
result Reveals the presence/absence of cohort effects in different populations.
Gene-Gene association for Imaging Genetics Data using Robust Kernel Canonical Correlation Analysisstat.ML
In genome-wide interaction studies, to detect gene-gene interactions, most methods are divided into two folds: single nucleotide polymorphisms (SNP) based and gene-based methods. Basically, the methods based on the gene are more effective than the methods based on a single SNP. Recent years, while the kernel canonical …
C-mix: a high dimensional mixture model for censored durations, with applications to genetic datastat.ML
We introduce a mixture model for censored durations (C-mix), and develop maximum likelihood inference for the joint estimation of the time distributions and latent regression parameters of the model. We consider a high-dimensional setting, with datasets containing a large number of biomedical covariates. We therefore p…
Missing data is an important challenge when dealing with high dimensional data arranged in the form of an array. In this paper, we propose methods for estimation of the parameters of array variate normal probability model from partially observed multiway data. The methods developed here are useful for missing data impu…
Method tackles missing covariates in large-scale datasets.
problem Cross-population missing data problem in large-scale datasets.
method Augmented transfer regression learning method combining importance-weighted estimating equations and imputation terms.
result Estimator is -consistent and asymptotically normal, attaining semiparametric efficiency bound under correct specification.
Proposes a convex method to estimate GGMs with covariates.
problem Improving conditional independence structure estimation with covariates.
method Convex optimization framework for joint estimation of mean and precision matrix.
result Improved theoretical guarantees and practical utility demonstrated.
Covariance-Insured Screeningstat.ML
Modern bio-technologies have produced a vast amount of high-throughput data with the number of predictors far greater than the sample size. In order to identify more novel biomarkers and understand biological mechanisms, it is vital to detect signals weakly associated with outcomes among ultrahigh-dimensional predictor…
In this work, a novel approach is proposed for joint analysis of high dimensional time-resolved cardiac motion features obtained from segmented cardiac MRI and low dimensional clinical risk factors to improve survival prediction in heart failure. Different methods are evaluated to find the optimal way to insert convent…
Paper proposes inference method for high-dimensional censored quantile regression.
problem Identifying heterogeneous effects of high-dimensional genetic biomarkers on survival outcomes.
method Combines low-dimensional model estimates based on multi-sample splittings and variable selection.
result Proposed estimator is consistent and asymptotically follows a Gaussian process.
ENN method uses expectile regression for genetic data analysis of complex diseases.
problem Discover additional genetic variants contributing to complex diseases.
method Developed an expectile neural network (ENN) method integrating expectile regression and neural networks.
result ENN method outperforms existing expectile regression in discovering genetic variants predisposing to sub-populations.
Semi-supervised GAN creates synthetic genetic data for disease prediction.
problem Expensive and time-consuming to build large labeled genetic databases.
method Semi-supervised Genetic Generative Adversarial Network (gGAN).
result Model achieved satisfactory results with real genetic data.
Efficiently infers graph edges from genetic similarity data in landscape genetics.
problem Inferring unknown graph edges from genetic similarity data in a heterogeneous landscape.
method Developed an efficient first-order optimization method to solve the inverse landscape genetics problem.
result Our method provides fast and reliable convergence, significantly outperforming existing heuristics.
Stein-Encoder isolates genetic signals in multi-modal biomedical data.
problem Integration of high-dimensional genomic data with clinical data obscures genetic predictive impact.
method White-box supervised framework using Stein's method and residualization.
result Stein-Encoder improves predictive accuracy and reveals specific biological mechanisms.
Discovering causal genetic variants from large genetic association studies poses many difficult challenges. Assessing which genetic markers are involved in determining trait status is a computationally demanding task, especially in the presence of gene-gene interactions. A non-parametric Bayesian approach in the form o…
FastCPH efficiently predicts survival times using neural networks.
problem Improving efficiency and accuracy of Cox proportional hazards models in neural networks.
method Developed FastCPH, a linear-time method supporting Breslow and Efron methods for tied events.
result Outperforms existing CoxPH approaches and selects useful covariates.
Genome-wide association studies (GWAS) have emerged as a rich source of genetic clues into disease biology, and they have revealed strong genetic correlations among many diseases and traits. Some of these genetic correlations may reflect causal relationships. We developed a method to quantify causal relationships betwe…
Novel tests for genetic independence in high-dimensional data.
problem Testing independence in genetics studies with many variables.
method Defining premetric structures on genetic data support spaces.
result Solid theoretical framework and computationally-efficient implementations.
As the complexity of neural network models has grown, it has become increasingly important to optimize their design automatically through metalearning. Methods for discovering hyperparameters, topologies, and learning rate schedules have lead to significant increases in performance. This paper shows that loss functions…
Deep models improve GWAS by identifying genetic interactions.
problem Missing non-linear interaction effects in GWAS.
method Gradient-based DeepLIFT technique to interpret deep models.
result Known and novel genetic risk factors identified.
We introduce GeNet, a method for shotgun metagenomic classification from raw DNA sequences that exploits the known hierarchical structure between labels for training. We provide a comparison with state-of-the-art methods Kraken and Centrifuge on datasets obtained from several sequencing technologies, in which dataset s…
Genetic algorithms have been widely used in many practical optimization problems. Inspired by natural selection, operators, including mutation, crossover and selection, provide effective heuristics for search and black-box optimization. However, they have not been shown useful for deep reinforcement learning, possibly …
New method uses DNN for genetic variant identification, controlling randomness and improving interpretability.
problem Challenges in interpreting deep neural networks for genetic variant identification.
method Interpretable neural network model with controlled variable selection using ensembling, knockoffs, and de-randomization.
result The proposed method leads to more discoveries compared to conventional methods.
To the best of our knowledge, there are no general well-founded robust methods for statistical unsupervised learning. Most of the unsupervised methods explicitly or implicitly depend on the kernel covariance operator (kernel CO) or kernel cross-covariance operator (kernel CCO). They are sensitive to contaminated data, …
Genetic sequence data are well described by hidden Markov models (HMMs) in which latent states correspond to clusters of similar mutation patterns. Theory from statistical genetics suggests that these HMMs are nonhomogeneous (their transition probabilities vary along the chromosome) and have large support for self tran…
Deep Genetic Networkcs.LG
Optimizing a neural network's performance is a tedious and time taking process, this iterative process does not have any defined solution which can work for all the problems. Optimization can be roughly categorized into - Architecture and Hyperparameter optimization. Many algorithms have been devised to address this pr…
A Consolidated Volatility Prediction with Back Propagation Neural Network and Genetic Algorithmq-fin.CP
Paper uses AI to predict stock market volatility with neural networks and genetic algorithms.
problem Traditional methods for predicting stock market volatility have high errors.
method Back-propagation neural network and genetic algorithm integrated model.
result The model predicts future volatility with low errors and high accuracy.
In plant and animal breeding studies a distinction is made between the genetic value (additive + epistatic genetic effects) and the breeding value (additive genetic effects) of an individual since it is expected that some of the epistatic genetic effects will be lost due to recombination. In this paper, we argue that t…
Ensemble GP improves genetic programming by achieving better results with smaller models.
problem Improving genetic programming for binary classification problems.
method Ensemble GP uses an evolved population structure, fitness evaluation, and genetic operators inspired by ensemble learning methods.
result Ensemble GP outperformed standard GP on eight binary classification problems, achieving better results with smaller models.
This paper compares Grid Search, Random Search, and Genetic Algorithm for NAS.
problem Hyperparameter optimization for neural architecture search.
method Comparison of Grid Search, Random Search, and Genetic Algorithm.
result Genetic Algorithm outperforms Grid Search and Random Search in terms of accuracy and execution time.
A genetic algorithm improves multivariate kernel density estimation.
problem Efficiently estimating multivariate kernel density functions.
method Genetic algorithm applied to subsamples of the original data.
result The genetic algorithm-based estimator performs better than traditional methods.
New method groups genetic data into coherent topics for disease insights.
problem Analyzing large, multi-dimensional genetic data sets.
method Conditional Hierarchical Bayesian Tucker Decomposition for genetic data analysis.
result Our models are more coherent than baseline models.
This paper improves dynamic hedging accuracy using genetic programming to forecast implied volatilities.
problem Improving the accuracy of dynamic hedging using implied volatilities.
method The paper uses genetic programming to forecast implied volatilities and tests the performance of these forecasts in dynamic hedging strategies.
result Genetic programming-generated implied volatilities improve hedging accuracy compared to static training methods.
For every group genetic code with finite number of generating and at most with one defining relation we introduce the braid group of this genetic code. This construction includes the braid group of Euclidean plane, the braid groups of closed orientable surfaces, B type groups of Artin-Brieskorn, and allow us to study a…
Link prediction is one of the fundamental problems in network analysis. In many applications, notably in genetics, a partially observed network may not contain any negative examples of absent edges, which creates a difficulty for many existing supervised learning approaches. We develop a new method which treats the obs…
Gradient GA uses gradient information to improve molecular design.
problem Random walk exploration limits genetic algorithms' quality and speed in molecular design.
method Gradient GA incorporates gradient information from the objective function into genetic algorithms, using a differentiable neural network and Discrete Langevin Proposal.
result Significantly improves convergence speed and solution quality over traditional genetic algorithms.
Proposes Genetic Thompson Sampling for multi-armed bandits, improving performance in nonstationary settings.
problem Improving sequential decision making tasks of online learning agents using multi-armed bandits.
method Integrates genetic principles into Thompson Sampling for multi-armed bandits.
result Significantly outperforms baselines in nonstationary settings.
EvoNUDGE uses graph neural networks to improve genetic programming performance.
problem Efficiency in evolutionary computation for problem solving.
method Graph neural network to elicit additional knowledge from symbolic regression problems.
result EvoNUDGE significantly outperforms conventional and neural genetic programming methods.
Locally epistatic genomic relationship matrices for genomic association, prediction and selectionstat.AP
As the amount and complexity of genetic information increases it is necessary that we explore some efficient ways of handling these data. This study takes the "divide and conquer" approach for analyzing high dimensional genomic data. Our aims include reducing the dimensionality of the problem that has to be dealt one a…
Proposes a new approach to MSDA by introducing latent covariate shift to handle varying label distributions.
problem Challenges of conventional MSDA approaches in real-world settings where label distributions vary across domains.
method Introduces latent covariate shift (LCS) and a causal generative model with latent noises, latent content variable, and latent style variable.
result Identifies latent content variable up to block identifiability, enabling more nuanced label distribution recovery.
Genome-wide association studies (GWAS) have achieved great success in the genetic study of Alzheimer's disease (AD). Collaborative imaging genetics studies across different research institutions show the effectiveness of detecting genetic risk factors. However, the high dimensionality of GWAS data poses significant cha…