Given genetic variations and various phenotypical traits, such as Magnetic Resonance Imaging (MRI) features, we consider two important and related tasks in biomedical research: i)to select genetic and phenotypical markers for disease diagnosis and ii) to identify associations between genetic and phenotypical data. Thes…
On-device research index
arXiv research
A locally-built, LLM-digested index of recent arXiv papers in quant finance, geometry/topology, and statistical ML — keyword search served straight from SQLite on this machine.
169,181 papers · 148 categories
Trend · papers per month
48 results for “genetic variation”
New methods improve genetic studies of complex diseases.
problem Improving genetic studies of complex diseases using high-dimensional clinical data.
method Evaluation of unsupervised disentangled representation learning methods (autoencoders, VAE, beta-VAE, FactorVAE) for genetic association studies.
result FactorVAEs and beta-VAEs outperform standard VAEs and non-variational autoencoders in genetic studies of asthma and COPD.
We utilize a recently developed genetic algorithm, in conjunction with discrete wavelets, for carrying out successful forecasts of the trend in financial time series, that includes the NASDAQ composite index. Discrete wavelets isolate the local, small scale variations in these non-stationary time series, after which th…
Characterizing and modeling cyclic behavior in non-stationary time series through multi-resolution analysisphysics.data-an
A method based on wavelet transform and genetic programming is proposed for characterizing and modeling variations at multiple scales in non-stationary time series. The cyclic variations, extracted by wavelets and smoothened by cubic splines, are well captured by genetic programming in the form of dynamical equations. …
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.
A Sparse Graph-Structured Lasso Mixed Model for Genetic Association with Confounding Correctioncs.LG
sGLMM corrects genetic associations with complex relatedness and confounding.
problem Correcting spurious associations in complex genetic data with population stratification and relatedness.
method Sparse graph-structured linear mixed model (sGLMM) that incorporates relatedness information and confounding correction.
result sGLMM outperforms existing approaches in modeling correlation from population structure and shared signals.
PDERL improves evolutionary reinforcement learning by using learning-based variation operators.
problem Scalability issue in Genetic Algorithms when combined with Deep Neural Networks.
method Integrates evolutionary and reinforcement learning through a hierarchical approach with learning-based variation operators.
result PDERL outperforms traditional evolutionary and reinforcement learning methods in robot locomotion tasks.
ContrastiveVI+ models CRISPR screens with noisy guide efficiency.
problem Noisy guide efficiency in CRISPR screens.
method Generative modeling framework that disentangles perturbation-induced from shared variations.
result ContrastiveVI+ better recovers perturbation-induced variations and identifies cells without edits.
Binacox: automatic cut-point detection in high-dimensional Cox model with applications in geneticsstat.ML
Binacox detects multiple cut-points in high-dimensional Cox models for genetic cancer data.
problem Detecting multiple cut-points in high-dimensional Cox models with many continuous features.
method Combines one-hot encoding with binarsity penalty for feature selection and regularization.
result Significantly outperforms state-of-the-art survival models in terms of C-index and computational speed.
CN-SBM clusters cancer samples and regions based on copy number variants.
problem Clonal evolution in cancer monitored by noisy copy number variants.
method Probabilistic framework using bipartite categorical block model.
result Improved model fit and clinically relevant subtypes identified.
In statistical genetics an important task involves building predictive models for the genotype-phenotype relationships and thus attribute a proportion of the total phenotypic variance to the variation in genotypes. Numerous models have been proposed to incorporate additive genetic effects into models for prediction or …
Advances of modern sensing and sequencing technologies generate a deluge of high dimensional space-temporal physiological and next-generation sequencing (NGS) data. Physiological traits are observed either as continuous random functions, or on a dense grid and referred to as function-valued traits. Both physiological a…
Fast and cheaper next generation sequencing technologies will generate unprecedentedly massive and highly-dimensional genomic and epigenomic variation data. In the near future, a routine part of medical record will include the sequenced genomes. A fundamental question is how to efficiently extract genomic and epigenomi…
DeepSequence model predicts mutation effects better than existing methods.
problem Quantifying complex interactions in biomolecules.
method Latent variable models with nonlinear dependencies.
result DeepSequence predicts mutation effects significantly better than site-independent or pairwise models.
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.
New model clusters cells and individuals, revealing genetic influences on cell types.
problem Clustering nested data with group-level and observation-level variables.
method Nested Atoms Model (NAM), Bayesian nonparametric approach.
result Identifies clusters of genetically similar individuals with homogeneous cell-type profiles.
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 distinguishes genetic correlations from causation in GWAS.
problem Identifying causal relationships among genetically correlated traits.
method Mixed fourth moments to quantify causal relationships.
result Identified 30 putative genetically causal relationships across 52 traits.
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…
GPO uses genetic algorithms for deep policy optimization in reinforcement learning.
problem Catastrophic consequence of parameter crossovers in neural networks for deep reinforcement learning.
method GPO uses imitation learning for policy crossover in the state space and applies policy gradient methods for mutation.
result GPO achieves superior performance and comparable sample efficiency compared to state-of-the-art policy gradient methods.
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.
Improved genetic programming by optimizing mutation operators for continuous program search.
problem Small syntactic mutations in genetic programming can lead to unpredictable behavioral shifts.
method Learned a compact trading-strategy DSL, created a block-factorized embedding, and designed geometry-compiled mutation operators.
result Geometry-compiled mutation operators discover strong strategies using fewer evaluations and achieve higher Sharpe ratios.
Deep Genetic Networkcs.LG
Introduces Deep Genetic Network for optimizing neural network hyperparameters.
problem Optimizing neural network hyperparameters is a tedious and time-consuming task.
method Uses genetic algorithms within a deep neural network architecture to optimize hyperparameters during training.
result Deep Genetic Network successfully optimizes hyperparameters in various types of neural network layers.
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.
GeNet classifies metagenomic sequences with less memory and comparable recall to state-of-the-art methods.
problem Classifying metagenomic sequences from raw DNA sequences.
method Exploits hierarchical structure between labels for training, using deep representations.
result GeNet achieves competitive precision and good recall with less memory requirements.
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.
Novel method prioritizes genetic variants in nonlinear models.
problem Variable selection in nonlinear and nonparametric regression.
method Developed RATE measure for summarizing variable importance.
result RATE explains improved predictive accuracy of nonlinear models.
Many complex disease syndromes such as asthma consist of a large number of highly related, rather than independent, clinical phenotypes, raising a new technical challenge in identifying genetic variations associated simultaneously with correlated traits. In this study, we propose a new statistical framework called grap…
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…
G2Ns combine genetic genes with neural networks for reinforcement learning.
problem Improving sample efficiency and performance in reinforcement learning.
method Genetic-Gated Networks (G2Ns) that integrate binary genetic genes with neural network hidden layers.
result G2Ns achieve significant improvements in sample efficiency and performance in reinforcement learning.
VERA uses variational inference to jailbreak LLMs without manual optimization.
problem Lack of principled objective for gradient-based optimization in jailbreaking LLMs.
method VERA casts black-box jailbreak prompting as a variational inference problem, training a small attacker LLM to approximate the target LLM's posterior over adversarial prompts.
result VERA achieves strong performance across various target LLMs, demonstrating the value of probabilistic inference for adversarial prompt generation.
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.
A multilevel model combines genetic and imaging data for AD diagnosis.
problem Classification from multimodal genetic and brain imaging data with unbalanced contributions.
method Multilevel model with structured penalties for joint effects between modalities.
result The model reveals relationships between genes, brain regions, and disease status.
Predict genetic inheritance patterns using hypergraphs and latent models.
problem Diagnosing inherited diseases requires identifying family genetic patterns.
method Represent family trees as hypergraphs, use latent state space models for causal inference.
result Allows for explainable predictions of patient genotypes based on relatives' phenotypes.
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.
Historical review of genetic algorithms for the TSP shows three distinct phases.
problem Optimizing routes for the Traveling Salesman Problem using genetic algorithms.
method Meta-data analysis of publications over time.
result Three distinct phases in the development of genetic algorithms for TSP identified.
Proposes new genetic algorithm rule for market competition.
problem Market competition genetic algorithm rules.
method Econophysics kinetic market model as an evolutionary algorithm.
result New replacement rule for genetic algorithms.
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.
Extracting Epistatic Interactions in Type 2 Diabetes Genome-Wide Data Using Stacked Autoencodercs.LG
Deep learning detects genetic interactions in type 2 diabetes.
problem Detecting genetic interactions in complex diseases like type 2 diabetes.
method Stacked Autoencoder for non-linear epistatic interactions.
result Deep learning can uncover missing heritability in complex diseases.
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.
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.
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.
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…
Motivation: Recent advances in technology for brain imaging and high-throughput genotyping have motivated studies examining the influence of genetic variation on brain structure. Wang et al. (Bioinformatics, 2012) have developed an approach for the analysis of imaging genomic studies using penalized multi-task regressi…
GADAM uses genetic algorithm to improve Adam's performance in deep learning.
problem Deep learning optimization stuck in local optima.
method GADAM combines Adam and genetic algorithm to evolve unit models.
result GADAM effectively avoids local optima and achieves faster convergence.