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.
ENN method uses expectile regression for genetic data analysis of complex diseases.
Semi-supervised GAN creates synthetic genetic data for disease prediction.
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 algorithm reconstructs genealogies from genetic data.
The paper develops methods to identify stable associations across multiple studies.
While linear mixed model (LMM) has shown a competitive performance in correcting spurious associations raised by population stratification, family structures, and cryptic relatedness, more challenges are still to be addressed regarding the complex structure of genotypic and phenotypic data. For example, geneticists hav…
New method detects change-points in population genetics.
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…
EvoNUDGE uses graph neural networks to improve genetic programming performance.
Ensemble learning is a powerful paradigm that has been usedin the top state-of-the-art machine learning methods like Random Forestsand XGBoost. Inspired by the success of such methods, we have devel-oped a new Genetic Programming method called Ensemble GP. The evo-lutionary cycle of Ensemble GP follows the same steps a…
Develops a GP framework for age and year-specific mortality surfaces.
Mathematical methods of population genetics and framework of exchangeability provide a Markov chain model for analysis and interpretation of stochastic behaviour of equity markets, explaining, in particular, market shape formation, statistical equilibrium and temporal stability of market weights.
Lapse-supported life insurance exacerbates adverse selection risks.
An evolutionary algorithm separates mixed DNA profiles in forensic genetics.
Proposes Genetic Thompson Sampling for multi-armed bandits, improving performance in nonstationary settings.
One primary task of population health analysis is the identification of risk factors that, for some subpopulation, have a significant association with some health condition. Examples include finding lifestyle factors associated with chronic diseases and finding genetic mutations associated with diseases in precision he…
The Interaction-Transformation (IT) is a new representation for Symbolic Regression that restricts the search space into simpler, but expressive, function forms. This representation has the advantage of creating a smoother search space unlike the space generated by Expression Trees, the common representation used in Ge…
With the development of high-throughput technologies, principal component analysis (PCA) in the high-dimensional regime is of great interest. Most of the existing theoretical and methodological results for high-dimensional PCA are based on the spiked population model in which all the population eigenvalues are equal ex…
U-aggregation combines multiple models without labels for better risk prediction.
Paper proposes a hybrid AI method to optimize pandemic actions.
EB-VAE combines tumor growth and dropout data for personalized treatment response modeling.
Method tackles missing covariates in large-scale datasets.
LEARNER improves low-rank matrix estimation using source population data.
Linear Mixed Models (LMMs) are important tools in statistical genetics. When used for feature selection, they allow to find a sparse set of genetic traits that best predict a continuous phenotype of interest, while simultaneously correcting for various confounding factors such as age, ethnicity and population structure…
CLSB models system dynamics from cross-sectional data with population-level regularization.
Individual's semantics have been used for guiding the learning process of Genetic Programming solving supervised learning problems. The semantics has been used to proposed novel genetic operators as well as different ways of performing parent selection. The latter is the focus of this contribution by proposing three he…
New method estimates high-dimensional GoM models efficiently.
MutaGAN predicts mutations of evolving protein populations using GANs.
ESAC combines genetic methods with RL to improve scalability and efficiency.
Probabilistic modeling is cyclical: we specify a model, infer its posterior, and evaluate its performance. Evaluation drives the cycle, as we revise our model based on how it performs. This requires a metric. Traditionally, predictive accuracy prevails. Yet, predictive accuracy does not tell the whole story. We propose…
We propose a new algorithm to do posterior sampling of Kingman's coalescent, based upon the Particle Markov Chain Monte Carlo methodology. Specifically, the algorithm is an instantiation of the Particle Gibbs Sampling method, which alternately samples coalescent times conditioned on coalescent tree structures, and tree…
Efficiently infers graph edges from genetic similarity data in landscape genetics.
A Bernoulli Mixture Model (BMM) is a finite mixture of random binary vectors with independent dimensions. The problem of clustering BMM data arises in a variety of real-world applications, ranging from population genetics to activity analysis in social networks. In this paper, we analyze the clusterability of BMMs from…
New model clusters cells and individuals, revealing genetic influences on cell types.
We introduce an evolutionary algorithm called recombinator--means for optimizing the highly non-convex kmeans problem. Its defining feature is that its crossover step involves all the members of the current generation, stochastically recombining them with a repurposed variant of the -means++ seeding algorithm. Th…
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…
We provide existence, uniqueness and stability results for affine stochastic Volterra equations with -kernels and jumps. Such equations arise as scaling limits of branching processes in population genetics and self-exciting Hawkes processes in mathematical finance. The strategy we adopt for the existence part is b…
This paper describes a new method for Symbolic Regression that allows to find mathematical expressions from a dataset. This method has a strong mathematical basis. As opposed to other methods such as Genetic Programming, this method is deterministic, and does not involve the creation of a population of initial solution…
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.
We study clustering methods for binary data, first defining aggregation criteria that measure the compactness of clusters. Five new and original methods are introduced, using neighborhoods and population behavior combinatorial optimization metaheuristics: first ones are simulated annealing, threshold accepting and tabu…
Latent variable models with hidden binary units appear in various applications. Learning such models, in particular in the presence of noise, is a challenging computational problem. In this paper we propose a novel spectral approach to this problem, based on the eigenvectors of both the second order moment matrix and t…
Deep models improve GWAS by identifying genetic interactions.
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.
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…
Approximate Bayesian computation (ABC) can be used for model fitting when the likelihood function is intractable but simulating from the model is feasible. However, even a single evaluation of a complex model may take several hours, limiting the number of model evaluations available. Modelling the discrepancy between t…