arXiv subjects

Federico Ferrari

Publications and source records attributed to Federico Ferrari.

15 recordsLinked to original sources

arXiv2025

A Matlab code for analysis and topology optimization with Third Medium Contact

We present a Matlab code for modelling and topology optimization of hyperelastic structures, including contact modelled by the Third Medium Contact (TMC) approach. By using the so-called HuHu-regularization we penalize the skew distortion of the bilinear finite elements discretizing void regions, thus promoting convergence of the nonlinear solver. First, we show how this method is implemented in a compact code, allowing to simulate contact and force transfer in hyperelastic structures. We then solve two topology optimization problems for minimum end-compliance of structures exhibiting contact. In the first example, contact happens at the supported boundary, while the second features self-contact. The Matlab scripts that replicate the results are included, and we discuss some possible extensions to more general problems.

cs.MS↗

arXiv2025

Leveraging External Data for Testing Experimental Therapies with Biomarker Interactions in Randomized Clinical Trials

In oncology the efficacy of novel therapeutics often differs across patient subgroups, and these variations are difficult to predict during the initial phases of the drug development process. The relation between the power of randomized clinical trials and heterogeneous treatment effects has been discussed by several authors. In particular, false negative results are likely to occur when the treatment effects concentrate in a subpopulation but the study design did not account for potential heterogeneous treatment effects. The use of external data from completed clinical studies and electronic health records has the potential to improve decision-making throughout the development of new therapeutics, from early-stage trials to registration. Here we discuss the use of external data to evaluate experimental treatments with potential heterogeneous treatment effects. We introduce a permutation procedure to test, at the completion of a randomized clinical trial, the null hypothesis that the experimental therapy does not improve the primary outcomes in any subpopulation. The permutation test leverages the available external data to increase power. Also, the procedure controls the false positive rate at the desired $\alpha$-level without restrictive assumptions on the external data, for example, in scenarios with unmeasured confounders, different pre-treatment patient profiles in the trial population compared to the external data, and other discrepancies between the trial and the external data. We illustrate that the permutation test is optimal according to an interpretable criteria and discuss examples based on asymptotic results and simulations, followed by a retrospective analysis of individual patient-level data from a collection of glioblastoma clinical trials.

stat.ME↗

arXiv2025

Optimization of the initial post-buckling response of trusses and frames by an asymptotic approach

Asymptotic post-buckling theory is applied to sizing and topology optimization of trusses and frames, exploring its potential and current computational difficulties. We show that a designs' post-buckling response can be controlled by including the lowest two asymptotic coefficients, representing the initial post-buckling slope and curvature, in the optimization formulation. This also reduces the imperfection sensitivity of the optimized design. The asymptotic expansion can further be used to approximate the structural nonlinear response, and then to optimize for a given measure of the nonlinear mechanical performance such as, for example, end-compliance or complementary work. Examples of linear and nonlinear compliance minimization of trusses and frames show the effective use of the asymptotic method for including post-buckling constraints in structural optimization.

cs.CE↗

arXiv2024

Bayesian Joint Additive Factor Models for Multiview Learning

It is increasingly common to collect data of multiple different types on the same set of samples. Our focus is on studying relationships between such multiview features and responses. A motivating application arises in the context of precision medicine where multi-omics data are collected to correlate with clinical outcomes. It is of interest to infer dependence within and across views while combining multimodal information to improve the prediction of outcomes. The signal-to-noise ratio can vary substantially across views, motivating more nuanced statistical tools beyond standard late and early fusion. This challenge comes with the need to preserve interpretability, select features, and obtain accurate uncertainty quantification. To address these challenges, we introduce two complementary factor regression models. A baseline Joint Factor Regression (\textsc{jfr}) captures combined variation across views via a single factor set, and a more nuanced Joint Additive FActor Regression (\textsc{jafar}) that decomposes variation into shared and view-specific components. For \textsc{jfr}, we use independent cumulative shrinkage process (\textsc{i-cusp}) priors, while for \textsc{jafar} we develop a dependent version (\textsc{d-cusp}) designed to ensure identifiability of the components. We develop Gibbs samplers that exploit the model structure and accommodate flexible feature and outcome distributions. Prediction of time-to-labor onset from immunome, metabolome, and proteome data illustrates performance gains against state-of-the-art competitors. Our open-source software (\texttt{R} package) is available at https://github.com/niccoloanceschi/jafar.

stat.ML↗

arXiv2024

Design optimization of advanced tow-steered composites with manufacturing constraints

Tow steering technologies, such as Automated fiber placement, enable the fabrication of composite laminates with curvilinear fiber, tow, or tape paths. Designers may therefore tailor tow orientations locally according to the expected local stress state within a structure, such that strong and stiff orientations of the tow are (for example) optimized to provide maximal mechanical benefit. Tow path optimization can be an effective tool in automating this design process, yet has a tendency to create complex designs that may be challenging to manufacture. In the context of tow steering, these complexities can manifest in defects such as tow wrinkling, gaps, overlaps. In this work, we implement manufacturing constraints within the tow path optimization formulation to restrict the minimum tow turning radius and the maximum density of gaps between and overlaps of tows. This is achieved by bounding the local value of the curl and divergence of the vector field associated with the tow orientations. The resulting local constraints are effectively enforced in the optimization framework through the Augmented Lagrangian method. The resulting optimization methodology is demonstrated by designing 2D and 3D structures with optimized tow orientation paths that maximize stiffness (minimize compliance) considering various levels of manufacturing restrictions. The optimized tow paths are shown to be structurally efficient and to respect imposed manufacturing constraints. As expected, the more geometrical complexity that can be achieved by the feedstock tow and placement technology, the higher the stiffness of the resulting optimized design.

cs.CE↗

arXiv2024

Optimal sizing of 1D vibrating columns accounting for axial compression and self-weight

We investigate the effect of axial compression on the optimal design of columns, for the maximization of the fundamental vibration frequency. The compression may be due to a force at the columns' tip or to a load distributed along its axis, which may act either independently or simultaneously. We discuss the influence of these contributions on the optimality conditions, and show how the optimal beam design, and the corresponding frequency gain drastically change with the level of compression. We also discuss the indirect effect of frequency optimization on the critical load factors for the tip ($\lambda_{P}$) and distributed ($\lambda_{Q}$) loads. Finally, we provide some quantitative results for the optimal design problem parametrized by the triple ($\lambda_{P}$, $\lambda_{Q}$, $\Omega^{2}$) of buckling and dynamic eigenvalues.

physics.class-ph↗

arXiv2021

Efficiently resolving rotational ambiguity in Bayesian matrix sampling with matching

A wide class of Bayesian models involve unidentifiable random matrices that display rotational ambiguity, with the Gaussian factor model being a typical example. A rich variety of Markov chain Monte Carlo (MCMC) algorithms have been proposed for sampling the parameters of these models. However, without identifiability constraints, reliable posterior summaries of the parameters cannot be obtained directly from the MCMC output. As an alternative, we propose a computationally efficient post-processing algorithm that allows inference on non-identifiable parameters. We first orthogonalize the posterior samples using Varimax and then tackle label and sign switching with a greedy matching algorithm. We compare the performance and computational complexity with other methods using a simulation study and chemical exposures data. The algorithm implementation is available in the infinitefactor R package on CRAN.

stat.CO↗

arXiv2021

Topology Optimization with linearized buckling criteria in 250 lines of Matlab

We present a 250 line Matlab code for topology optimization for linearized buckling criteria. The code is conceived to handle stiffness, volume and Buckling Load Factors (BLFs) either as the objective function or as constraints. We use the Kreisselmeier-Steinhauser aggregation function in order to reduce multiple objectives (viz. constraints) to a single, differentiable one. Then, the problem is sequentially approximated by using MMA-like expansions and an OC-like scheme is tailored to update the variables. The inspection of the stress stiffness matrix leads to a vectorized implementation for its efficient construction and for the sensitivity analysis of the BLFs. This, coupled with the efficiency improvements already presented by Ferrari and Sigmund 2020, cuts all the computational bottlenecks associated with setting up the buckling analysis and allows buckling topology optimization problems of an interesting size to be solved on a laptop. The efficiency and flexibility of the code is demonstrated over a few structural design examples and some ideas are given for possible extensions.

math.OC↗

arXiv2020

Revisiting element removal for density-based structural topology optimization with reintroduction by Heaviside projection

We present a strategy grounded in the element removal idea of Bruns and Tortorelli [1] and aimed at reducing computational cost and circumventing potential numerical instabilities of density-based topology optimization. The design variables and the relative densities are both represented on a fixed, uniform finite element grid, and linked through filtering and Heaviside projection. The regions in the analysis domain where the relative density is below a specified threshold are removed from the forward analysis and replaced by fictitious nodal boundary conditions. This brings a progressive cut of the computational cost as the optimization proceeds and helps to mitigate numerical instabilities associated with low-density regions. Removed regions can be readily reintroduced since all the design variables remain active and are modeled in the formal sensitivity analysis. A key feature of the proposed approach is that the Heaviside functions promote material reintroduction along the structural boundaries by amplifying the magnitude of the sensitivities inside the filter reach. Several 2D and 3D structural topology optimization examples are presented, including linear and nonlinear compliance minimization, the design of a force inverter, and frequency and buckling load maximization. The approach is shown to be effective at producing optimized designs equivalent or nearly equivalent to those obtained without the element removal, while providing remarkable computational savings.

math.NA↗

arXiv2020

A new generation 99 line Matlab code for compliance Topology Optimization and its extension to 3D

Compact and efficient Matlab implementations of compliance Topology Optimization (TO) for 2D and 3D continua are given, consisting of 99 and 125 lines respectively. On discretizations ranging from $3\cdot 10^{4}$ to $4.8\cdot10^{5}$ elements, the 2D version, named top99neo, shows speedups from 2.55 to 5.5 times compared to the well-known top88 code (Andreassen-etal 2011). The 3D version, named top3D125, is the most compact and efficient Matlab implementation for 3D TO to date, showing a speedup of 1.9 times compared to the code of Amir-etal 2014, on a discretization with $2.2\cdot10^{5}$ elements. For both codes, improvements are due to much more efficient procedures for the assembly and implementation of filters and shortcuts in the design update step. The use of an acceleration strategy, yielding major cuts in the overall computational time, is also discussed, stressing its easy integration within the basic codes.

cs.CE↗

arXiv2020

Identifying main effects and interactions among exposures using Gaussian processes

This article is motivated by the problem of studying the joint effect of different chemical exposures on human health outcomes. This is essentially a nonparametric regression problem, with interest being focused not on a black box for prediction but instead on selection of main effects and interactions. For interpretability, we decompose the expected health outcome into a linear main effect, pairwise interactions, and a non-linear deviation. Our interest is in model selection for these different components, accounting for uncertainty and addressing non-identifability between the linear and nonparametric components of the semiparametric model. We propose a Bayesian approach to inference, placing variable selection priors on the different components, and developing a Markov chain Monte Carlo (MCMC) algorithm. A key component of our approach is the incorporation of a heredity constraint to only include interactions in the presence of main effects, effectively reducing dimensionality of the model search. We adapt a projection approach developed in the spatial statistics literature to enforce identifiability in modeling the nonparametric component using a Gaussian process. We also employ a dimension reduction strategy to sample the non-linear random effects that aids the mixing of the MCMC algorithm. The proposed MixSelect framework is evaluated using a simulation study, and is illustrated using data from the National Health and Nutrition Examination Survey (NHANES). Code is available on GitHub.

stat.AP↗

arXiv2020

Towards solving large scale topology optimization problems with buckling constraints at the cost of linear analyses

This work presents a multilevel approach to large--scale topology optimization accounting for linearized buckling criteria. The method relies on the use of preconditioned iterative solvers for all the systems involved in the linear buckling and sensitivity analyses and on the approximation of buckling modes from a coarse discretization. The strategy shows three main benefits: first, the computational cost for the eigenvalue analyses is drastically cut. Second, artifacts due to local stress concentrations are alleviated when computing modes on the coarse scale. Third, the ability to select a reduced set of important global modes and filter out less important local ones. As a result, designs with improved buckling resistance can be generated with a computational cost little more than that of a corresponding compliance minimization problem solved for multiple loading cases. Examples of 2D and 3D structures discretized by up to some millions of degrees of freedom are solved in Matlab to show the effectiveness of the proposed method. Finally, a post--processing procedure is suggested in order to reinforce the optimized design against local buckling.

math.NA↗

arXiv2020

Bayesian Factor Analysis for Inference on Interactions

This article is motivated by the problem of inference on interactions among chemical exposures impacting human health outcomes. Chemicals often co-occur in the environment or in synthetic mixtures and as a result exposure levels can be highly correlated. We propose a latent factor joint model, which includes shared factors in both the predictor and response components while assuming conditional independence. By including a quadratic regression in the latent variables in the response component, we induce flexible dimension reduction in characterizing main effects and interactions. We propose a Bayesian approach to inference under this Factor analysis for INteractions (FIN) framework. Through appropriate modifications of the factor modeling structure, FIN can accommodate higher order interactions and multivariate outcomes. We provide theory on posterior consistency and the impact of misspecifying the number of factors. We evaluate the performance using a simulation study and data from the National Health and Nutrition Examination Survey (NHANES). Code is available on GitHub.

stat.ME↗

arXiv2019

Nonparametric Bayesian multi-armed bandits for single cell experiment design

The problem of maximizing cell type discovery under budget constraints is a fundamental challenge for the collection and analysis of single-cell RNA-sequencing (scRNA-seq) data. In this paper, we introduce a simple, computationally efficient, and scalable Bayesian nonparametric sequential approach to optimize the budget allocation when designing a large scale experiment for the collection of scRNA-seq data for the purpose of, but not limited to, creating cell atlases. Our approach relies on the following tools: i) a hierarchical Pitman-Yor prior that recapitulates biological assumptions regarding cellular differentiation, and ii) a Thompson sampling multi-armed bandit strategy that balances exploitation and exploration to prioritize experiments across a sequence of trials. Posterior inference is performed by using a sequential Monte Carlo approach, which allows us to fully exploit the sequential nature of our species sampling problem. We empirically show that our approach outperforms state-of-the-art methods and achieves near-Oracle performance on simulated and scRNA-seq data alike. HPY-TS code is available at https://github.com/fedfer/HPYsinglecell.

stat.AP↗

arXiv2018

Revisiting topology optimization with buckling constraints

We review some features of topology optimization with a lower bound on the critical load factor, as computed by linearized buckling analysis. The change of the optimized design, the competition between stiffness and stability requirements and the activation of several buckling modes, depending on the value of such lower bound, are studied. We also discuss some specific issues which are of particular interest for this problem, as the use of non-conforming finite elements for the analysis, the use of inconsistent sensitivities in the optimization and the replacement of the single eigenvalue constraints with an aggregated measure. We discuss the influence of these practices on the optimization result, giving some recommendations.

math.NA↗