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…
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.
168,695 papers · 148 categories
Trend · papers per month
48 results for “Genetic Sequences”
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…
New KNN test improves association analysis of high-dimensional sequencing data.
problem Challenges in using neural networks for high-dimensional sequencing data analysis.
method Kernel-based neural network (KNN) test for complex association analysis.
result KNN test outperforms SKAT in detecting non-linear and interaction effects.
BoGA combines evolutionary search with Bayesian optimization for efficient protein design.
problem Designing novel proteins with specific characteristics is challenging due to sequence space complexity.
method BoGA integrates a genetic algorithm with Bayesian optimization to efficiently explore sequence space.
result BoGA accelerates discovery of high-confidence binders for diverse protein design objectives.
A New Statistical Framework for Genetic Pleiotropic Analysis of High Dimensional Phenotype Datastat.ML
The widely used genetic pleiotropic analysis of multiple phenotypes are often designed for examining the relationship between common variants and a few phenotypes. They are not suited for both high dimensional phenotypes and high dimensional genotype (next-generation sequencing) data. To overcome these limitations, we …
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…
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.
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…
New algorithm reconstructs genealogies from genetic data.
problem Reconstructing genealogies from genetic data.
method Iterative algorithm {\sc Rec-Gen} for pedigrees from a generative model.
result Accurate reconstruction of a large fraction of pedigrees with low sample complexity.
BOAT optimizes multiple antibody properties efficiently.
problem Balancing multiple drug-like properties in antibody design.
method Bayesian optimization framework coupling surrogate modeling and genetic algorithm.
result Competitive performance with state-of-the-art multi-objective protein optimization methods.
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…
Study investigates how preprocessing, feature selection, and model selection affect performance on imbalanced genetic data.
problem Challenges in using machine learning on imbalanced genetic datasets.
method Comparative analysis of data preprocessing, feature selection techniques, and machine learning models on imbalanced genetic data.
result Class-imbalanced target variables and skewed predictors have little to no impact on classification performance.
Paper proposes a hybrid AI method to optimize pandemic actions.
problem Optimizing government actions to balance public health and economy.
method Combines Deep Q-Learning and Genetic Algorithms for optimal sequences of actions.
result Deep Q-Learning outperforms Genetic Algorithms in optimizing action sequences.
Second generation sequencing technologies are being increasingly used for genetic association studies, where the main research interest is to identify sets of genetic variants that contribute to various phenotype. The phenotype can be univariate disease status, multivariate responses and even high-dimensional outcomes.…
For precision medicine and personalized treatment, we need to identify predictive markers of disease. We focus on Alzheimer's disease (AD), where magnetic resonance imaging scans provide information about the disease status. By combining imaging with genome sequencing, we aim at identifying rare genetic markers associa…
A test for neural networks identifies genetic associations.
problem Testing complex associations in neural networks.
method Sieve quasi-likelihood ratio test for neural networks with one hidden layer.
result The test statistic has an asymptotic chi-squared distribution.
New RL approach builds short ancestral recombination graphs.
problem Building short ancestral recombination graphs (ARGs).
method Reinforcement Learning applied to genetic sequences.
result RL can build ARGs as short as heuristic algorithms.
DNA sequencing to identify genetic variants is becoming increasingly valuable in clinical settings. Assessment of variants in such sequencing data is commonly implemented through Bayesian heuristic algorithms. Machine learning has shown great promise in improving on these variant calls, but the input for these is still…
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.
Edit distance, also known as Levenshtein distance, is an essential way to compare two strings that proved to be particularly useful in the analysis of genetic sequences and natural language processing. However, edit distance is a discrete function that is known to be hard to optimize. This fact hampers the use of this …
The functions of proteins and RNAs are determined by a myriad of interactions between their constituent residues, but most quantitative models of how molecular phenotype depends on genotype must approximate this by simple additive effects. While recent models have relaxed this constraint to also account for pairwise in…
LaMBO optimizes biological sequences using autoencoders and Bayesian optimization.
problem Bayesian optimization for drug design is limited by discrete, high-dimensional decision variables.
method Jointly trains denoising autoencoder with a Gaussian process head for gradient-based optimization in latent space.
result LaMBO outperforms genetic optimizers and requires no large pretraining corpus.
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…
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.
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.
Each human genome is a 3 billion base pair set of encoding instructions. Decoding the genome using deep learning fundamentally differs from most tasks, as we do not know the full structure of the data and therefore cannot design architectures to suit it. As such, architectures that fit the structure of genomics should …
Sequential decision making is a typical problem in reinforcement learning with plenty of algorithms to solve it. However, only a few of them can work effectively with a very small number of observations. In this report, we introduce the progress to learn the policy for Malaria Control as a Reinforcement Learning proble…
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 …
Single individual haplotyping is an NP-hard problem that emerges when attempting to reconstruct an organism's inherited genetic variations using data typically generated by high-throughput DNA sequencing platforms. Genomes of diploid organisms, including humans, are organized into homologous pairs of chromosomes that d…
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…
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.
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…
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.
A Likelihood-Free Inference Framework for Population Genetic Data using Exchangeable Neural Networkscs.LG
An explosion of high-throughput DNA sequencing in the past decade has led to a surge of interest in population-scale inference with whole-genome data. Recent work in population genetics has centered on designing inference methods for relatively simple model classes, and few scalable general-purpose inference techniques…
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…
Attention Routing: track-assignment detailed routing using attention-based reinforcement learningcs.LG
A new router uses attention-based reinforcement learning to solve detailed routing problems efficiently.
problem Solving detailed routing in integrated circuits while adhering to complex design rules.
method Attention-based reinforcement learning applied to track-assignment detailed routing.
result The attention router achieves over 100x acceleration compared to a genetic router without sacrificing solution quality.
GEGL uses genetic experts to improve deep learning for molecular design.
problem Designing molecules with desired properties using deep learning.
method Genetic expert-guided learning (GEGL) framework for training DNN.
result Significantly improves molecular design, achieving high scores on benchmarks.
Transposable Elements (TEs) or jumping genes are the DNA sequences that have an intrinsic capability to move within a host genome from one genomic location to another. Studies show that the presence of a TE within or adjacent to a functional gene may alter its expression. TEs can also cause an increase in the rate of m…
Genetic algorithms optimize neural networks for cosmological data analysis.
problem Inaccurate results from neural networks due to poor hyperparameter selection.
method Used genetic algorithms to optimize hyperparameters of neural networks.
result Genetic algorithms improve neural network performance in cosmological data analysis.