Vahid Babaei

Navid Ansari, Alireza Javanmardi, Eyke Hüllermeier et al.

Bayesian optimization (BO) provides a powerful framework for optimizing black-box, expensive-to-evaluate functions. It is therefore an attractive tool for engineering design problems, typically involving multiple objectives. Thanks to the rapid advances in fabrication and measurement methods as well as parallel computing infrastructure, querying many design problems can be heavily parallelized. This class of problems challenges BO with an unprecedented setup where it has to deal with very large batches, shifting its focus from sample efficiency to iteration efficiency. We present a novel Bayesian optimization framework specifically tailored to address these limitations. Our key contribution is a highly scalable, sample-based acquisition function that performs a non-dominated sorting of not only the objectives but also their associated uncertainty. We show that our acquisition function in combination with different Bayesian neural network surrogates is effective in data-intensive environments with a minimal number of iterations. We demonstrate the superiority of our method by comparing it with state-of-the-art multi-objective optimizations. We perform our evaluation on two real-world problems -- airfoil design and 3D printing -- showcasing the applicability and efficiency of our approach. Our code is available at: https://github.com/an-on-ym-ous/lbn_mobo

Navid Ansari, Hans-Peter Seidel, Nima Vahidi Ferdowsi et al.

Neural networks are powerful surrogates for numerous forward processes. The inversion of such surrogates is extremely valuable in science and engineering. The most important property of a successful neural inverse method is the performance of its solutions when deployed in the real world, i.e., on the native forward process (and not only the learned surrogate). We propose Autoinverse, a highly automated approach for inverting neural network surrogates. Our main insight is to seek inverse solutions in the vicinity of reliable data which have been sampled form the forward process and used for training the surrogate model. Autoinverse finds such solutions by taking into account the predictive uncertainty of the surrogate and minimizing it during the inversion. Apart from high accuracy, Autoinverse enforces the feasibility of solutions, comes with embedded regularization, and is initialization free. We verify our proposed method through addressing a set of real-world problems in control, fabrication, and design.

Jiahong Wang, Logan Numerow, Stelian Coros et al.

Graph neural networks (GNNs) have emerged as a versatile and efficient option for modeling the dynamic behavior of deformable materials. While GNNs generalize readily to arbitrary shapes, mesh topologies, and material parameters, existing architectures struggle to correctly predict the temporal evolution of key physical quantities such as linear and angular momentum. In this work, we propose MomentumGNN -- a novel architecture designed to accurately track momentum by construction. Unlike existing GNNs that output unconstrained nodal accelerations, our model predicts per-edge stretching and bending impulses which guarantee the preservation of linear and angular momentum. We train our network in an unsupervised fashion using a physics-based loss, and we show that our method outperforms baselines in a number of common scenarios where momentum plays a pivotal role.

Kevin Tirta Wijaya, Michael Sun, Minghao Guo et al.

Accurate prediction of continuous properties is essential to many scientific and engineering tasks. Although deep-learning regressors excel with abundant labels, their accuracy deteriorates in data-scarce regimes. We introduce RankRefine, a model-agnostic, plug-and-play post hoc method that refines regression with expert knowledge coming from pairwise rankings. Given a query item and a small reference set with known properties, RankRefine combines the base regressor's output with a rank-based estimate via inverse variance weighting, requiring no retraining. In molecular property prediction task, RankRefine achieves up to 10% relative reduction in mean absolute error using only 20 pairwise comparisons obtained through a general-purpose large language model (LLM) with no finetuning. As rankings provided by human experts or general-purpose LLMs are sufficient for improving regression across diverse domains, RankRefine offers practicality and broad applicability, especially in low-data settings.

Navid Ansari, Hans-Peter Seidel, Vahid Babaei

This paper introduces a novel and scalable framework for uncertainty estimation and separation with applications in data driven modeling in science and engineering tasks where reliable uncertainty quantification is critical. Leveraging an ensemble of quantile regression (E-QR) models, our approach enhances aleatoric uncertainty estimation while preserving the quality of epistemic uncertainty, surpassing competing methods, such as Deep Ensembles (DE) and Monte Carlo (MC) dropout. To address challenges in separating uncertainty types, we propose an algorithm that iteratively improves separation through progressive sampling in regions of high uncertainty. Our framework is scalable to large datasets and demonstrates superior performance on synthetic benchmarks, offering a robust tool for uncertainty quantification in data-driven applications.

Kevin Tirta Wijaya, Minghao Guo, Michael Sun et al.

Molecular deep learning models have achieved remarkable success in property prediction, but they often require large amounts of labeled data. The challenge is that, in real-world applications, labels are extremely scarce, as obtaining them through laboratory experimentation is both expensive and time-consuming. In this work, we introduce MoleVers, a versatile pretrained molecular model designed for various types of molecular property prediction in the wild, i.e., where experimentally-validated labels are scarce. MoleVers employs a two-stage pretraining strategy. In the first stage, it learns molecular representations from unlabeled data through masked atom prediction and extreme denoising, a novel task enabled by our newly introduced branching encoder architecture and dynamic noise scale sampling. In the second stage, the model refines these representations through predictions of auxiliary properties derived from computational methods, such as the density functional theory or large language models. Evaluation on 22 small, experimentally-validated datasets demonstrates that MoleVers achieves state-of-the-art performance, highlighting the effectiveness of its two-stage framework in producing generalizable molecular representations for diverse downstream properties.

Kevin Tirta Wijaya, Navid Ansari, Hans-Peter Seidel et al.

Data-driven generation of molecules with desired properties, also known as inverse molecular design (IMD), has attracted significant attention in recent years. Despite the significant progress in the accuracy and diversity of solutions, existing IMD methods lag behind in terms of trustworthiness. The root issue is that the design process of these methods is increasingly more implicit and indirect, and this process is also isolated from the native forward process (NFP), the ground-truth function that models the molecular dynamics. Following this insight, we propose TrustMol, an IMD method built to be trustworthy. For this purpose, TrustMol relies on a set of technical novelties including a new variational autoencoder network. Moreover, we propose a latent-property pairs acquisition method to effectively navigate the complexities of molecular latent optimization, a process that seems intuitive yet challenging due to the high-frequency and discontinuous nature of molecule space. TrustMol also integrates uncertainty-awareness into molecular latent optimization. These lead to improvements in both explainability and reliability of the IMD process. We validate the trustworthiness of TrustMol through a wide range of experiments.

Navid Ansari, Hans-Peter Seidel, Vahid Babaei

In computational design and fabrication, neural networks are becoming important surrogates for bulky forward simulations. A long-standing, intertwined question is that of inverse design: how to compute a design that satisfies a desired target performance? Here, we show that the piecewise linear property, very common in everyday neural networks, allows for an inverse design formulation based on mixed-integer linear programming. Our mixed-integer inverse design uncovers globally optimal or near optimal solutions in a principled manner. Furthermore, our method significantly facilitates emerging, but challenging, combinatorial inverse design tasks, such as material selection. For problems where finding the optimal solution is not desirable or tractable, we develop an efficient yet near-optimal hybrid optimization. Eventually, our method is able to find solutions provably robust to possible fabrication perturbations among multiple designs with similar performances.