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.
Neural GDEs improve graph prediction by blending discrete structures and differential equations.
Gene regulatory networks play a crucial role in controlling an organism's biological processes, which is why there is significant interest in developing computational methods that are able to extract their structure from high-throughput genetic data. A typical approach consists of a series of conditional independence t…
VEGN uses graph neural networks to predict disease-causing mutations from genetic variants.
Gene regulatory networks play a crucial role in controlling an organism's biological processes, which is why there is significant interest in developing computational methods that are able to extract their structure from high-throughput genetic data. Many of these computational methods are designed to infer individual …
Quantitatively predicting phenotype variables by the expression changes in a set of candidate genes is of great interest in molecular biology but it is also a challenging task for several reasons. First, the collected biological observations might be heterogeneous and correspond to different biological mechanisms. Seco…
A new method for joint eQTL mapping and gene network estimation.
Oscillations lie at the core of many biological processes, from the cell cycle, to circadian oscillations and developmental processes. Time-keeping mechanisms are essential to enable organisms to adapt to varying conditions in environmental cycles, from day/night to seasonal. Transcriptional regulatory networks are one…
Convolutional neural networks learn effective summary statistics for ABC inference.
Networks have in recent years emerged as an invaluable tool for describing and quantifying complex systems in many branches of science. Recent studies suggest that networks often exhibit hierarchical organization, where vertices divide into groups that further subdivide into groups of groups, and so forth over multiple…
ENN method uses expectile regression for genetic data analysis of complex diseases.
Semi-supervised GAN creates synthetic genetic data for disease prediction.
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…
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…
Paper uses AI to predict stock market volatility with neural networks and genetic algorithms.
Due to the dynamic nature of biological systems, biological networks underlying temporal process such as the development of {\it Drosophila melanogaster} can exhibit significant topological changes to facilitate dynamic regulatory functions. Thus it is essential to develop methodologies that capture the temporal evolut…
New method uses DNN for genetic variant identification, controlling randomness and improving interpretability.
This paper begins with considering the identification of sparse linear time-invariant networks described by multivariable ARX models. Such models possess relatively simple structure thus used as a benchmark to promote further research. With identifiability of the network guaranteed, this paper presents an identificatio…
EvoNUDGE uses graph neural networks to improve genetic programming performance.
Genetic algorithms optimize neural networks for cosmological data analysis.
TNDE quantifies dynamic gene drivers from single-cell snapshots.
DASH simplifies neural networks for gene regulatory dynamics using domain knowledge.
Efficiently infers gene regulatory networks from spatial data.
InfoSEM infers gene regulatory networks without GT labels, improving performance.
There has been significant recent interest towards achieving highly efficient deep neural network architectures. A promising paradigm for achieving this is the concept of evolutionary deep intelligence, which attempts to mimic biological evolution processes to synthesize highly-efficient deep neural networks over succe…
New method designs multilayer nanoparticles using AI.
Deep models improve GWAS by identifying genetic interactions.
Develops probabilistic models for gene regulatory network inference.
We introduce the Genetic-Gated Networks (G2Ns), simple neural networks that combine a gate vector composed of binary genetic genes in the hidden layer(s) of networks. Our method can take both advantages of gradient-free optimization and gradient-based optimization methods, of which the former is effective for problems …
Efficiently infers graph edges from genetic similarity data in landscape genetics.
Reconstructing transcriptional regulatory networks is an important task in functional genomics. Data obtained from experiments that perturb genes by knockouts or RNA interference contain useful information for addressing this reconstruction problem. However, such data can be limited in size and/or are expensive to acqu…
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 …
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 …
Constructing gene regulatory networks is a critical step in revealing disease mechanisms from transcriptomic data. In this work, we present NO-BEARS, a novel algorithm for estimating gene regulatory networks. The NO-BEARS algorithm is built on the basis of the NOTEARS algorithm with two improvements. First, we propose …
Gradient GA uses gradient information to improve molecular design.
This paper compares Grid Search, Random Search, and Genetic Algorithm for NAS.
In recent years, deep learning methods applying unsupervised learning to train deep layers of neural networks have achieved remarkable results in numerous fields. In the past, many genetic algorithms based methods have been successfully applied to training neural networks. In this paper, we extend previous work and pro…
A test for neural networks identifies genetic associations.
Deep learning and genetic algorithms speed up cosmological Bayesian inference.
We present a Bayesian hierarchical multi-view mixture model termed Symphony that simultaneously learns clusters of cells representing cell types and their underlying gene regulatory networks by integrating data from two views: single-cell gene expression data and paired epigenetic data, which is informative of gene-gen…
SEISM tests neural network features for regulatory genomics.
Deep neural network learning can be formulated as a non-convex optimization problem. Existing optimization algorithms, e.g., Adam, can learn the models fast, but may get stuck in local optima easily. In this paper, we introduce a novel optimization algorithm, namely GADAM (Genetic-Evolutionary Adam). GADAM learns deep …
Networks of coupled dynamical systems provide a powerful way to model systems with enormously complex dynamics, such as the human brain. Control of synchronization in such networked systems has far reaching applications in many domains, including engineering and medicine. In this paper, we formulate the synchronization…
Regshock visualizes financial risks to help regulators manage systemic shocks.
As an increasing number of genome-wide association studies reveal the limitations of attempting to explain phenotypic heritability by single genetic loci, there is growing interest for associating complex phenotypes with sets of genetic loci. While several methods for multi-locus mapping have been proposed, it is often…
Study improves chiral photonic metasurface design using neural networks and genetic algorithms.
GEGL uses genetic experts to improve deep learning for molecular design.
LAGE is a systematic framework developed in Java. The motivation of LAGE is to provide a scalable and parallel solution to reconstruct Gene Regulatory Networks (GRNs) from continuous gene expression data for very large amount of genes. The basic idea of our framework is motivated by the philosophy of divideand-conquer.…
New KNN test improves association analysis of high-dimensional sequencing data.