Correspondence between neuroevolution and gradient descent
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ABSTRACT:
SUBMITTER: Whitelam S
PROVIDER: S-EPMC8563972 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Recent research in machine learning pointed to the core problem of state-of-the-art models which impedes their widespread adoption in different domains. The models' inability to differentiate between noise and subtle, yet significant variation in data leads to their vulnerability to adversarial perturbations that cause wrong predictions with high confidence. The study is aimed at identifying whether the algorithms inspired by biological evolution may achieve better results in cases where brittle robustness properties are highly sensitive to the slight noise. To answer this question, we introduce the new robust gradient descent inspired by the stability and adaptability of biological systems to unknown and changing environments. The proposed optimization technique involves an open-ended adaptation process with regard to two hyperparameters inherited from the generalized Verhulst population growth equation. The hyperparameters increase robustness to adversarial noise by penalizing the degree to which hardly visible changes in gradients impact prediction. The empirical evidence on synthetic and experimental datasets confirmed the viability of the bio-inspired gradient descent and suggested promising directions for future research. The code used for computational experiments is provided in a repository at https://github.com/yukinoi/bio_gradient_descent.
| S-EPMC6611597 | biostudies-literature
Project description:BackgroundGene Regulatory Networks (GRNs) have become a major focus of interest in recent years. Elucidating the architecture and dynamics of large scale gene regulatory networks is an important goal in systems biology. The knowledge of the gene regulatory networks further gives insights about gene regulatory pathways. This information leads to many potential applications in medicine and molecular biology, examples of which are identification of metabolic pathways, complex genetic diseases, drug discovery and toxicology analysis. High-throughput technologies allow studying various aspects of gene regulatory networks on a genome-wide scale and we will discuss recent advances as well as limitations and future challenges for gene network modeling. Novel approaches are needed to both infer the causal genes and generate hypothesis on the underlying regulatory mechanisms.MethodologyIn the present article, we introduce a new method for identifying a set of optimal gene regulatory pathways by using structural equations as a tool for modeling gene regulatory networks. The method, first of all, generates data on reaction flows in a pathway. A set of constraints is formulated incorporating weighting coefficients. Finally the gene regulatory pathways are obtained through optimization of an objective function with respect to these weighting coefficients. The effectiveness of the present method is successfully tested on ten gene regulatory networks existing in the literature. A comparative study with the existing extreme pathway analysis also forms a part of this investigation. The results compare favorably with earlier experimental results. The validated pathways point to a combination of previously documented and novel findings.ConclusionsWe show that our method can correctly identify the causal genes and effectively output experimentally verified pathways. The present method has been successful in deriving the optimal regulatory pathways for all the regulatory networks considered. The biological significance and applicability of the optimal pathways has also been discussed. Finally the usefulness of the present method on genetic engineering is depicted with an example.
| S-EPMC2933224 | biostudies-literature
Project description:Stein variational gradient descent (SVGD) is a particle-based inference algorithm that leverages gradient information for efficient approximate inference. In this work, we enhance SVGD by leveraging preconditioning matrices, such as the Hessian and Fisher information matrix, to incorporate geometric information into SVGD updates. We achieve this by presenting a generalization of SVGD that replaces the scalar-valued kernels in vanilla SVGD with more general matrix-valued kernels. This yields a significant extension of SVGD, and more importantly, allows us to flexibly incorporate various preconditioning matrices to accelerate the exploration in the probability landscape. Empirical results show that our method outperforms vanilla SVGD and a variety of baseline approaches over a range of real-world Bayesian inference tasks.
| S-EPMC6923147 | biostudies-literature
Project description:Overparametrized deep networks predict well, despite the lack of an explicit complexity control during training, such as an explicit regularization term. For exponential-type loss functions, we solve this puzzle by showing an effective regularization effect of gradient descent in terms of the normalized weights that are relevant for classification.
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Project description:This paper considers the analysis of continuous time gradient-based optimization algorithms through the lens of nonlinear contraction theory. It demonstrates that in the case of a time-invariant objective, most elementary results on gradient descent based on convexity can be replaced by much more general results based on contraction. In particular, gradient descent converges to a unique equilibrium if its dynamics are contracting in any metric, with convexity of the cost corresponding to the special case of contraction in the identity metric. More broadly, contraction analysis provides new insights for the case of geodesically-convex optimization, wherein non-convex problems in Euclidean space can be transformed to convex ones posed over a Riemannian manifold. In this case, natural gradient descent converges to a unique equilibrium if it is contracting in any metric, with geodesic convexity of the cost corresponding to contraction in the natural metric. New results using semi-contraction provide additional insights into the topology of the set of optimizers in the case when multiple optima exist. Furthermore, they show how semi-contraction may be combined with specific additional information to reach broad conclusions about a dynamical system. The contraction perspective also easily extends to time-varying optimization settings and allows one to recursively build large optimization structures out of simpler elements. Extensions to natural primal-dual optimization and game-theoretic contexts further illustrate the potential reach of these new perspectives.
| S-EPMC7402485 | biostudies-literature
Project description:MotivationThe increasing availability of complete genomes demands for models to study genomic variability within entire populations. Pangenome graphs capture the full genomic similarity and diversity between multiple genomes. In order to understand them, we need to see them. For visualization, we need a human readable graph layout: A graph embedding in low (e.g. two) dimensional depictions. Due to a pangenome graph's potential excessive size, this is a significant challenge.ResultsIn response, we introduce a novel graph layout algorithm: the Path-Guided Stochastic Gradient Descent (PG-SGD). PG-SGD uses the genomes, represented in the pangenome graph as paths, as an embedded positional system to sample genomic distances between pairs of nodes. This avoids the quadratic cost seen in previous versions of graph drawing by Stochastic Gradient Descent (SGD). We show that our implementation efficiently computes the low dimensional layouts of gigabase-scale pangenome graphs, unveiling their biological features.AvailabilityWe integrated PG-SGD in ODGI which is released as free software under the MIT open source license. Source code is available at https://github.com/pangenome/odgi.
| S-EPMC10542513 | biostudies-literature
Project description:[This corrects the article DOI: 10.1371/journal.pone.0236661.].
| S-EPMC7714173 | biostudies-literature
Project description:Although the literature on the relationship between economic growth and CO2 emissions is extensive, the use of machine learning (ML) tools remains seminal. In this paper, we assess this nexus for Italy using innovative algorithms, with yearly data for the 1960-2017 period. We develop three distinct models: the batch gradient descent (BGD), the stochastic gradient descent (SGD), and the multilayer perceptron (MLP). Despite the phase of low Italian economic growth, results reveal that CO2 emissions increased in the predicting model. Compared to the observed statistical data, the algorithm shows a correlation between low growth and higher CO2 increase, which contradicts the main strand of literature. Based on this outcome, adequate policy recommendations are provided.
| S-EPMC8458215 | biostudies-literature
Project description:Electron cryomicroscopy (cryo-EM) is an imaging technique widely used in structural biology to determine the three-dimensional structure of biological molecules from noisy two-dimensional projections with unknown orientations. As the typical pipeline involves processing large amounts of data, efficient algorithms are crucial for fast and reliable results. The stochastic gradient descent (SGD) algorithm has been used to improve the speed of ab initio reconstruction, which results in a first, low-resolution estimation of the volume representing the molecule of interest, but has yet to be applied successfully in the high-resolution regime, where expectation-maximization algorithms achieve state-of-the-art results, at a high computational cost. In this article, we investigate the conditioning of the optimization problem and show that the large condition number prevents the successful application of gradient descent-based methods at high resolution. Our results include a theoretical analysis of the condition number of the optimization problem in a simplified setting where the individual projection directions are known, an algorithm based on computing a diagonal preconditioner using Hutchinson's diagonal estimator, and numerical experiments showing the improvement in the convergence speed when using the estimated preconditioner with SGD. The preconditioned SGD approach can potentially enable a simple and unified approach to ab initio reconstruction and high-resolution refinement with faster convergence speed and higher flexibility, and our results are a promising step in this direction.
| S-EPMC10705587 | biostudies-literature
Project description:BackgroundStochastic effects can be important for the behavior of processes involving small population numbers, so the study of stochastic models has become an important topic in the burgeoning field of computational systems biology. However analysis techniques for stochastic models have tended to lag behind their deterministic cousins due to the heavier computational demands of the statistical approaches for fitting the models to experimental data. There is a continuing need for more effective and efficient algorithms. In this article we focus on the parameter inference problem for stochastic kinetic models of biochemical reactions given discrete time-course observations of either some or all of the molecular species.ResultsWe propose an algorithm for inference of kinetic rate parameters based upon maximum likelihood using stochastic gradient descent (SGD). We derive a general formula for the gradient of the likelihood function given discrete time-course observations. The formula applies to any explicit functional form of the kinetic rate laws such as mass-action, Michaelis-Menten, etc. Our algorithm estimates the gradient of the likelihood function by reversible jump Markov chain Monte Carlo sampling (RJMCMC), and then gradient descent method is employed to obtain the maximum likelihood estimation of parameter values. Furthermore, we utilize flux balance analysis and show how to automatically construct reversible jump samplers for arbitrary biochemical reaction models. We provide RJMCMC sampling algorithms for both fully observed and partially observed time-course observation data. Our methods are illustrated with two examples: a birth-death model and an auto-regulatory gene network. We find good agreement of the inferred parameters with the actual parameters in both models.ConclusionsThe SGD method proposed in the paper presents a general framework of inferring parameters for stochastic kinetic models. The method is computationally efficient and is effective for both partially and fully observed systems. Automatic construction of reversible jump samplers and general formulation of the likelihood gradient function makes our method applicable to a wide range of stochastic models. Furthermore our derivations can be useful for other purposes such as using the gradient information for parametric sensitivity analysis or using the reversible jump samplers for full Bayesian inference. The software implementing the algorithms is publicly available at http://cbcl.ics.uci.edu/sgd.
| S-EPMC2914651 | biostudies-literature